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From naïve pluripotency to chimeras: a new ethical challenge?

Posted by , on 18 December 2014

This article by Insoo Hyun was first published in  Development. Also read the companion ethics article here.

 
In recent years, there has been much interest in the prospect of generating and using human stem cells that exhibit a state of naïve pluripotency. Such a pluripotent state might be functionally confirmed by assessing the chimeric contribution of these cells to non-human blastocysts. Furthermore, the generation of naïve human pluripotent stem cells in vitro could lead to the creation of chimeric animal models that can facilitate the study of human development and disease. However, these lines of research raise thorny ethical concerns about the moral status of such chimeric animals. Here, I call attention to these ethical barbs and suggest away in which to proceed cautiously.

 

In pursuit of naïve pluripotency It has become a prevailing view among stem cell researchers that pluripotency is not a singular state but rather a spectrum that ranges from ‘naïve’ to more developmentally ‘primed’ states (Hackett and Surani, 2014). Stem cells are considered to be ‘naïve’ if they are free of developmental biases, with ‘ground state’ stem cells being the least developmentally and epigenetically constrained. By contrast, ‘primed’ pluripotent stem cells are more committed toward lineage specific developmental programs and are epigenetically restricted (Nichols and Smith, 2009). These distinctions underlie the differences between human embryonic stem cells (ESCs) and those derived from mouse blastocysts; human ESCs correspond more closely to primed mouse epiblast stem cells (EpiSCs), which are derived from the epiblast of the post implantation stage mouse embryo (Brons et al., 2007; Tesar et al., 2007). An important research question is thus whether human pluripotent stem cells, including ESCs and induced pluripotent stem cells (iPSCs), can be converted to a naïve state under culture conditions, and recent studies (Gafni et al., 2013;Ware et al., 2014; Takashima et al., 2014; Theunissen et al., 2014) suggest that this is indeed possible. The generation and maintenance of such naïve human pluripotent stem cells in vitro could lead to the creation of better chimeric animal models that would facilitate the study of human development and disease and possibly allow purer populations of specialized cells to be developed for regenerative therapies.

However, one of the major challenges standing in theway of these goals is that there is not yet a universal test for defining and confirming the naïve pluripotent state of human stem cells (Hackett and Surani, 2014). Whereas molecular benchmarks, such as global gene expression profiles and global DNA hypomethylation, are undoubtedly important, researchers are keen to find a functional basis for designating naïve status to human stem cells. In the case of mouse ESCs, naïve pluripotency is functionally confirmed by generating intra species chimeras in which the ESCs are marked/tagged and injected into viable mouse blastocysts that are then implanted back into the mouse uterus. If the resulting mouse pups contain derivatives of these tagged cells in all their organ systems, the injected stem cells are confirmed as being truly naïve. Could a chimeric murine-host test offer a defining standard for naïve pluripotency in human cells?

The answer appears to be no. Although one research group reported that interspecies chimeras could be generated by injecting their derived naïve pluripotent human stem cells into mouse morulae (Gafni et al., 2013), another group attempted to repeat this chimeric assay but were not able to succeed (Theunissen et al., 2014). Alternative approaches using animal species closer to humans might thus have to be attempted in order to assess whether lab-generated naïve pluripotent human stem cells can further differentiate and contribute to all tissues in vivo. Whereas naïve iPSCs were recently reported to have been derived from rhesus monkey fibroblasts and were used to create chimeric rhesus-mouse preimplantation embryos (Fang et al., 2014), researchers will undoubtedly want go beyond non-human primate cells to test the functional capabilities of naïve pluripotent human stem cells in vivo through the gestation of interspecies chimeras. But what are the appropriate ethical considerations for these kinds of human-to-non human experiments?

 

Concerns about naïve pluripotent stem cell-generated chimeras

The ethics of human-to-non-human chimera research has received much attention in recent years, driven in large part by the imagined possibilities of extreme interspecies chimerism that stem cell-based approaches might afford over other, less developmentally based types of chimeras, such as human tumor grafting in adult nude mice (Behringer, 2007). Up to now, people’s fears about human/nonhuman
chimerism were confined by the fact that researchers had only ‘primed’ human pluripotent stem cells at their disposal. The advent of naïve pluripotent human stem cells, however, could tilt the possibilities far more toward the realization of extreme human/non human chimerism. The scientific prospect of the latter is, after all, one of the anticipated research benefits of using naïve pluripotent human stem cells to create better (i.e. more biologically humanized) chimeric animal models of human development and disease, and possibly even to generate transplantable human organs in large animal species, as discussed by Göran Hermerén elsewhere in this issue (Rashid et al., 2014; Hermerén, 2015).

As long as researchers pursue their interest in naïve pluripotency, the prospect of extreme interspecies chimerism looms on the horizon. Some members of the lay public might worry that the radical biological humanization of animals could lead to their moral humanization, thus elevating these beings to a level of protected moral status that is not possessed by other types of laboratory animals (Streiffer, 2005). One chimera study has already raised eyebrows in the media: mice containing human glial cells in their brains were reported to perform memory and learning tests much faster than control mice, raising the specter that such ‘humanized’ mice might be cognitively enhanced (Han et al., 2013). If moral humanization were to accompany biological humanization in research chimeras, would we have reasons to prohibit either the development of new naïve human pluripotency assays in nonhuman hosts or the generation of extreme chimeras for research?

This question is not readily accommodated by existing institutional regulations and stem cell research guidelines. Whereas all in vivo chimera studies are overseen by institutional animal research committees, these committees are tasked with focusing on animal welfare and study design issues, not with questions about the moral status of the generated chimeras (National Research Council, 1996). Furthermore, stem cell-specific professional guidelines issued by the International Society for Stem Cell Research (ISSCR) only address the impermissibility of transferring any products of research involving human pluripotent or totipotent cells into a human or non-human primate uterus (ISSCR, 2006; http://www.isscr.org/docs/defaultsource/hesc-guidelines/isscrhescguidelines2006.pdf ). Aside from gestation efforts in human and non-human primate surrogates, all other chimera research is potentially allowable, subject to review by the appropriate animal research and stem cell committees.

 

Recommending a path forward

The ISSCR Ethics and Public Policy Committee has issued an advisory report that provides a framework for overseeing chimera research (Hyun et al., 2007). The Committee’s approach attempts to build on current animal research welfare principles, but incorporates stem cell-specific expertise to consider the developmental effects of human stem cell-based chimerism on animal welfare. This stepwise approach is consistent with Hermerén’s recommendation that regulating bodies ought to avoid constructing entirely new ethical frameworks for every new area of science (Hermerén, 2015). Critics might complain, however, that the Committee’s report does nothing to address the worry that naïve human pluripotent stem cells could be used to create extreme human/non-human chimerism, particularly in the central nervous systems, of animal hosts that are evolutionarily closer to humans. What if researchers propose to create extreme neurological chimeras that subsequently could end up with a moral status that approximates or is equal to ours? Merely extending animal welfare principles to these types of neurological chimeras seems insufficient to address people’s ethical concerns. In response to this worry, two key issues must be addressed and clarified.

First, we should seriously question the underlying assumption that the biological humanization of animals could lead to their moral humanization. The important issue here is not whether chimerism could produce the appearance of human-like characteristics in animal hosts tout court, but rather whether these human-like characteristics serve as the basis for our moral status as human beings. Perhaps a leading candidate for such a status-conferring characteristic is ‘self-consciousness’, defined as one’s ability to perceive oneself as a temporally extended being who is the subject of one’s own experiences. Philosophers typically believe that this type of awareness requires subjects to be language users, as self consciousness must involve recursive thinking (i.e. thinking about thinking) or at least having a higher-order mental awareness of one’s own mental states (Allen and Bekoff, 1997). No animals to date, however, not even non-human primates, have been proven to be language users that can express their beliefs propositionally (Chomsky, 1980; Pinker, 1994). Added to these formidable limitations is the fact that self-consciousness is a complex mental faculty that takes years to emerge in human infants under the nurturing conditions of our everyday socialization processes. Chimeric research animals will not be raised within the “bosom of society” (to use Rousseau’s memorable phrase) and thus, regardless of their level or nature of chimerism, will not have the supporting conditions necessary to facilitate the emergence of self consciousness, as I have argued extensively elsewhere (Hyun, 2013). Others might object that the response above misses an important point. That is, as long as acute neurological chimerism were to confer enough of the structural features of a humanized brain to biologically support self-consciousness in host animals, then it would be wrong to deny these animals this potential by failing to rear them in conditions that would support the eventual emergence of self-consciousness. This hypothetical complaint brings me to the second point that requires clarification.

In chimera ethics debates, it is very common to try to identify one or more human-like traits that are believed to be necessary and sufficient to confer a threshold level of protected moral status. We can call this the ‘mathematical classical set’ approach, whereby membership in a set is defined by the possession of one or more characteristic properties that are common to all members of the set and are not shared by any entities that are not members. The problem with taking a classical set approach to moral status is that it is bound to leave out individuals whom we would otherwise want to include as having protected moral status – be they newborns, the cognitively disabled or the senile elderly who might lack self-consciousness (to use the sample trait discussed above). A better approach, in my opinion, is to view moral membership as a ‘fuzzy set’, in which moral status is not absolutely dependent on having a single characteristic or set of characteristics, but rather is a category with membership that is dependent on any of a large group of attributes. This is the way people tend to conceptualize social categories such as parenthood, and biological entities such as immunoglobulins (Greenspan, 2001), and I propose, without having the space to defend the point fully here, that questions of moral status should be approached in a similar manner. In summary, people’s concerns about the possible emergent higher moral status of chimeric animals presuppose a simple reductionist view of what it takes to be a member of our common moral community. These concerns disregard the richer array of attributes we actually draw upon when recognizing the moral status of those around us.

With these two clarifying points in mind, I recommend that the best path forward with regards to naïve pluripotent stem cell-based chimera research is to keep the regulatory and ethical focus firmly on animal welfare considerations, with the degree of animal welfare at stake being dependent on the physical and mental attributes of the animal; we should be far less concerned about the emergence of moral humanity in chimeric animals.

 

References
Allen, C. and Bekoff, M. (1997). Species of Mind: the Philosophy and Biology of Cognitive Ethology. Cambridge, MA: MIT Press.

Behringer, R. R. (2007). Human-animal chimeras in biomedical research. Cell Stem Cell 1, 259-262.

Brons, I. G. M., Smithers, L. E., Trotter, M.W. B., Rugg-Gunn, P., Sun, B., Chuva de Sousa Lopes, S. M., Howlett, S. K., Clarkson, A., Ahrlund-Richter, L., Pedersen, R. A. et al. (2007). Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature 448, 191-195.

Chomsky, N. (1980). Human language and other semiotic systems. In Speaking of Apes: a Critical Anthology of Two-Way Communication with Man (ed. T. A.Sebeok and J. Umiker-Sebeok), pp. 429-440. New York: Plenum Press.

Fang, R., Liu, K., Zhao, Y., Li, H., Zhu, D., Du, Y., Xiang, C., Li, X., Liu, H., Miao, Z. et al. (2014). Generation of naïve induced pluripotent stem cells from rhesus monkey fibroblasts. Cell Stem Cell 15, 488-496.

Gafni, O., Weinberger, L., Mansour, A. A., Manor, Y. S., Chomsky, E., Ben-Yosef, D., Kalma, Y., Viukov, S., Maza, I., Zviran, A. et al. (2013). Derivation of novel human ground state naïve pluripotent stem cells. Nature 504, 282-286.

Greenspan, N. S. (2001). Dimensions of antigen recognition and levels of immunological specificity. Adv. Cancer Res. 80, 147-187.

Hackett, J. A. and Surani, M. A. (2014). Regulatory principles of pluripotency: from the ground state up. Cell Stem Cell 15, 416-430.

Han, X., Chen, M., Wang, F., Windrem, M., Wang, S., Shanz, S., Xu, Q., Oberheim, N. A., Bekar, L., Betstadt, S. et al. (2013). Forebrain engraftment by human glial progenitor cells enhances synaptic plasticity and learning in adult mice. Cell Stem Cell 12, 342-353.

Hermerén, G. (2015). Ethical considerations in chimera research. Development  142, 3-5.

Hyun, I. (2013). Bioethics and the Future of Stem Cell Research. New York: Cambridge University Press.

Hyun, I., Taylor, P., Testa, G., Dickens, B., Jung, K. W., McNab, A., Robertson, J., Skene, L. and Zoloth, L. (2007). Ethical standards for human-to-animal chimera experiments in stem cell research. Cell Stem Cell 1, 159-163.

International Society for Stem Cell Research (ISSCR) (2006). Guidelines for the conduct of human embryonic stem cell research?. National Research Council (1996). Guide for the Care and Use of Laboratory Animals. Washington, DC: National Academies Press.

Nichols, J. and Smith, A. (2009). Naïve and primed pluripotent states. Cell Stem Cell 4, 487-492.

Pinker, S. (1994). The Language Instinct: How the Mind Creates Language. New York: W. Morrow and Co.

Rashid, T., Kobayashi, T. and Nakauchi, H. (2014). Revisiting the flight of Icarus: making human organs from PSCs with large animal chimeras. Cell Stem Cell 15, 406-409.

Streiffer, R. (2005). At the edge of humanity: human stem cells, chimeras, and moral status. Kennedy Inst. Ethics J. 15, 347-370.

Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W. et al. (2014). Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158, 1254-1269.

Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J., Evans, E. P., Mack, D. L., Gardner, R. L. and McKay, R. D. G. (2007). New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 448, 196-199.

Theunissen, T.W., Powell, B. E.,Wang, H., Mitalipova, M., Faddah, D. A., Reddy, J., Fan, Z. P., Maetzel, D., Ganz, K., Shi, L. et al. (2014). Systematic identification of culture conditions for induction and maintenance of naïve human pluripotencyCell Stem Cell 15, 471-487.

Ware, C. B., Nelson, A. M., Mecham, B., Hesson, J., Zhou, W., Jonlin, E. C., Jimenez-Caliani, A. J., Deng, X., Cavanaugh, C., Cook, S. et al. (2014). Derivation of naïve human embryonic stem cells. Proc. Natl. Acad. Sci. USA 111, 4484-4489.

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Ethical considerations in chimera research

Posted by , on 18 December 2014

This article by Göran Hermerén was first published in  Development. Also read the companion ethics article  here.

 

The development of human pluripotent stem cells has opened up the possibility to analyse the function of human cells and tissues in animal hosts, thus generating chimeras. Although such lines of research have great potential for both basic and translational science, they also raise unique ethical issues that must be considered.

 

A major goal in life science research is to understand human development, physiology and dysfunction, as this will allow better treatment of disease and injury. However, our ability to conduct research using human subjects or samples is obviously limited. In recent years, the isolation of human embryonic stem cells [hESCs; (Thomson et al., 1998)] and the generation of human induced pluripotent stem cells [hIPSCs (Takahashi et al., 2007)] have opened new avenues to study human biology, but there is a need to analyse these cells in an in vivo setting. Consequently, many researchers are now turning to human-animal chimera research.

Lensch et al. (2007) have proposed the following definition of ‘chimera’: “The term chimera […] indicates organisms comprised of cells from two or more individuals of the same or different species. Today, the most common usage describes cellular combinations at the preimplantation blastocyst stage of development, […] also […] other entities created by introducing cells at later stages, including in adult recipients.” This definition makes it clear that there are different kinds of chimeras. This is also obvious from the definition proposed by Behringer (2007): “A chimera is an individual composed of somatic and, in certain cases, germ line tissues derived from more than one zygote. […] If the donor tissue and recipient are of different species, then an interspecific or cross-species chimera is generated.” Different kinds of human-animal chimeras might raise different ethical issues – according, for example, to which tissues the human cells contribute to or how long the chimeric animal survives. Chimeras that include human neural tissue are of particular concern, because the cognitive capacities of the chimeras might be affected, and because of the prevailing special status of humans in our culture.

In this Spotlight article, I will first summarise some of the recent research that uses chimeras, to provide a context for the subsequent discussion on the ethical issues surrounding this kind of research. I then provide a proposal for how such challenges can be addressed – so as to allow research to proceed while respecting these ethical concerns.

 

Current research avenues using chimeras

Several broad categories of experimental investigation are now making use of human-animal chimeras. Recent work from Jacob Hanna’s lab has used the mouse embryo as an in vivo system to test the potential of human pluripotent cells: creating chimeras by microinjection of hESCs or iPSCs into a mouse morula and analysing the chimeric embryo shortly afterwards (Gafni et al., 2013). Given that these experiments were limited to early embryos (10 days; within the limit allowed for research on human embryos), the ethical concerns here are limited, but it is possible that central nervous system (CNS) tissue containing both mouse and human cells will be found in this chimera.

In a different approach, the EU-funded project ‘Health and the Understanding of Metabolism, Aging and Nutrition’ (HUMAN; http://www.fp7human.eu/) proposes to address the problem of the increased frequency of metabolic diseases in an aging population by creating ‘humanised’ mouse models with cells from the liver and pancreas of human donors. In this way, it will be possible to study the functions of genes in human organs and how, in combination with factors like eating habits and nutrition, they can influence the risk of contracting a metabolic disease. The idea is to study and compare two different groups, namely very old healthy individuals and individuals with metabolic diseases. In contrast to the experiments described above, in which chimeric embryos were destroyed soon after creation, the HUMAN project involves maintaining chimeric animals until old age.

From an ethical standpoint, two avenues of research are particularly interesting: the creation of complete human organs in animals, and the generation of CNS, particularly forebrain, chimeras. The long-term goal of the first approach is to grow organs made exclusively from human cells in a chimeric animal, such as a pig, that could potentially be used for organ transplant. This goal has been pursued most actively by the research group of Hiro Nakauchi, focusing primarily on the pancreas (Kobayashi et al., 2010, 2014; Matsunari et al., 2012; Usui et al., 2012; Rashid et al., 2014), although it still remains at the hypothetical stage.

The second line is exemplified by the research of Steven Goldman and collaborators, who established mice in which the forebrain glial cells were completely replaced by human glia (Han et al., 2013). These animals manifested significantly different cognitive capabilities – showing enhanced plasticity and learning. Repeating such experiments with glia derived from individual patients with neuropsychiatric disorders could allow a better understanding of the pathology of such diseases and might aid in the identification of potential therapeutic targets. The fact that the humanised mice displayed apparently enhanced cognitive capacity raises particular ethical questions, discussed further below.

 

Ethical issues of chimera research

The examples discussed above suggest that at least two categories of chimera research need to be separated, as they raise partly different ethical issues: in vitro studies using early embryos, and in vivo studies involving sentient animals. The latter raises additional issues of animal health and welfare.

One key ethical question is whether crossing species boundaries is in principle or prima facie ethically wrong. If so, we need to consider whether the generation of stem cell chimeras represents a particular and controversial instance of such boundary crossing. The reason why such issues are raised is that humans and animals are treated differently in our culture and have different ethical and legal status: animals are not legal entities and do not have rights in the way that humans do.

One of the tacit premises in this discussion is that we view ourselves as distinct, and we must consider what defines a human being. Of course, in the history of western civilization, scientific discoveries have challenged and changed our view of ourselves. To begin with, it is necessary then to make some sort of distinction between being human as a biological concept and as a moral concept. In the latter case, the focus is on intentional action, self reflection and self-understanding: on humans as moral and responsible agents.

Concerning the goal of growing human organs in animals such as pigs (as discussed above), a key challenge is the xenogenic barrier – these two species are estimated to have diverged almost 100 million years ago, so is it even feasible to use a pig as an ‘incubator’ for human organs? If this barrier cannot be overcome, could we use primates? Or, taking this to the extreme, might one even conceive of using people in a permanent vegetative state or suffering from senile dementia (who might not display the key characteristics of intentional action, self-reflection and self understanding mentioned above) as incubators? This might
sound like science fiction or a dystopia, but should be discussed before it becomes scientifically feasible.

Two types of particularly problematic research are when cognitive capacities are changed and when germ-line effects are introduced (in which the potential exists for the production of human embryos in animals or vice versa). Thus, focus in the ethics discussion should be on chimeras in which changes have been introduced that might affect their cognitive capacities, and in cases in which the mixture between species is so extensive that confusion might arise as to which species the chimeric individual (and/or its germline) belongs to.

What ethical issues do these research avenues raise, over and above those concerning animal health and welfare? A possible list of concerns (e.g. see Danish Council of Ethics, 2008; and Streiffer, 2010) includes: violation of human dignity; violation of the order of nature; risk and scientific uncertainty; violation of the dignity of the humanised animal; violation of taboo against mixing of species; danger of moral confusion – should resulting chimeras be treated as animals or as humans? Some of these concerns might seem irrelevant: for instance, human dignity is obviously a property of humans, not of human cells, and thus may not apply to chimeric animals. However, it is crucial to examine carefully the arguments for and against particular lines of research, if only to avoid the impression that important issues are swept under the carpet. Important underlying values for those who are pursuing this research include safety and efficacy. Certainly both are valid concerns, but they do not always go together: a particular intervention can be safe but not effective, or effective but not safe.

Subtle ethical questions are raised by how uncertainties and risks in this type of research are to be handled. Proposals have been made as to how germline contribution could be avoided (e.g. the use of progenitor rather than stem cells), but do we know for sure that using progenitors will prevent the introduction of changes in the germline that are inherited? It is always possible to say that no inherited changes have been demonstrated in the experiments conducted so far, but that does not prove that this will never happen. When is ‘safe where to draw a line here is not ethically neutral; it might create opportunities for some and harm and/or difficulties for others.

To make ethically appropriate decisions on whether specific lines of research should be undertaken, we have to try to answer the following four questions: What do we know? What do we want? What are we able to do? What ought to be done? The answers to the first three questions are relevant to, but do not decide, the answer to the crucial fourth question. For instance, we may know something about the attitudes of people towards various aspects of research, but direct inferences from these attitudes cannot be made, as they might be based on incorrect or misleading information, which scientists have a responsibility to correct.

The key focus of ethics is conflicts of values, taken in a wide, non-technical sense, including interests, rights, liberties and obligations. The answer to the question ‘what ought to be done’ has to be informed by the answers to the previous ones, but decided on the basis of the values at stake, ordered in normative importance. However, it should be borne in mind that this analysis might be complicated by the simple fact that ‘we’ might know, want and be able to do different things, depending on the situation and context (discussed in Hermerén, 2014).

 

A strategy for addressing ethical challenges 

What is the best strategy to use in dealing with the ethical challenges raised by chimera research? In addition to the more general strategy developed elsewhere and alluded to above for dealing with ethical concerns, I propose that the following general precepts should be heeded in this particular research area: first, I recommend that one should avoid developing new ethical frameworks or rules for every new type of research. Where possible, it is advisable to use existing frameworks, unless there is something specific about the research that calls for changes in the existing framework. As far as possible, similar cases ought to be treated in similar ways.

Protection of animal welfare will obviously be important for in vivo studies, but what is required in addition to that? And how do we balance the need to limit regulatory hurdles against the importance of ensuring ethical compliance? In contrast to the National Academy of Science panel recommendations (National Research Council, 2005), the International Society for Stem Cell Research (ISSCR) guidelines 2008 (http://www.isscr.org/docs/default-source/clin-trans-guidelines/isscrglclinicaltrans.pdf ) stipulate that the assay of hESCs by teratoma formation should be accepted as routine and be exempt from Stem Cell Research Oversight (SCRO) review.

Why should these assays be exempt? Lensch et al. (2007) have argued that human teratoma formation studies in adult mice are justifiable and should be routinely approved by animal care committees with a minimal need for regulation by the stem cell research oversight process. Their main reason is that “the need for teratoma assays with hESCs is compelling” and that “we believe that the risk of inadvertently creating a rodent chimera with higher, human brain function is negligible.” However, this latter point needs to be discussed against the recent findings by Goldman and collaborators (Han et al., 2013), as discussed above. In particular, this research has shed light on the relative importance of niche and environment versus the origin of the transplanted cells – which defines the final phenotype? This case is also interesting in that the research indicated a cognitive improvement in the transplanted mice. Of course, this result is dependent on the methods of measurement and the criteria used for cognitive improvement, but it is worth discussing in relation to the ISSCR guidelines, which are according to previous studies’ safe enough? The decision about presented and discussed by Insoo Hyun elsewhere in this issue (Hyun, 2015).

 

Precaution or proportionality?

My personal view is that the precautionary principle has played too important a role in discussions on what should or should not be permitted in terms of chimera research, at least if it is interpreted as saying that, if there is a risk, you should do nothing. Inaction may also be risky and can lead to harm: if we adopt a no-risk scenario, medical research will be stifled and progress will be impossible. Instead, I would advocate some version of the principle of proportionality (Hermerén, 2012). I argue that the risk-benefit analysis can be improved by considering the following questions: Is the research objective important? Are the methods to achieve them feasible and are the facilities adequate? Are there no less risky or controversial methods available? Do the relevant personnel have the training required to deal with the research equipment and the animals?

If the answer to these questions is ‘yes’, then the research should be approved, but with appropriate caveats. Sensible precautions might include using progenitors rather than pluripotent cells, and treating the humanised mice as one would treat genetically modified crop: keep them isolated, make sure they do not mate with wild mice and euthanise them when the research is concluded.

 

Concluding remarks

Ethical problems arise in a context of beliefs and values. If people have different beliefs about current and future trends, and do not want to achieve and/or avoid the same goals, they will view the problem landscape differently. What is a problem to one person may not be to another. Time is then required for dialogues between the different stakeholders, including researchers, regulators, patients and organizations. In general, issues can not be settled once and for all, for the simple reason that research is developing rapidly, values and preferences change, and so do perceptions of risks and benefits. Top-down approaches must be avoided, as experience shows that they rarely work. Those who are worried must be allowed to express their concerns and in that sense participate in the setting of the agenda.

The advent of pluripotent stem cells and the use of chimera research have unearthed new ethical challenges, but with these approaches to hand, research should be able to proceed without excessive regulation.

 

References
Behringer, R. R. (2007). Human-animal chimeras in biomedical research. Cell Stem Cell 1, 259-262.

Danish Council of Ethics (2008). Man or Mouse? Ethical aspects of chimaera research. Copenhagen, Denmark.

Gafni, O., Weinberger, L., Mansour, A. A., Manor, Y. S., Chomsky, E., Ben-Yosef, D., Kalma, Y., Viukov, S., Maza, I., Zviran, A. et al. (2013). Derivation of novel human ground state naive pluripotent stem cells. Nature 504, 282-286.

Han, X., Chen, M., Wang, F., Windrem, M., Wang, S., Shanz, S., Xu, Q., Oberheim, N. A., Bekar, L., Betstadt, S. et al. (2013). Forebrain engraftment by human glial progenitor cells enhances synaptic plasticity and learning in adult mice. Cell Stem Cell 12, 342-353.

Hermerén, G. (2012). The principle of proportionality revisited: interpretations and applications. Med. Health Care Philos. 15, 373-382.

Hermerén, G. (2014). Human stem-cell research in gastroenterology: experimental treatment, tourism and biobanking. Best Pract. Res. Clin. Gastroenterol. 28, 257-268.

Hyun, I., Taylor, P., Testa, G., Dickens, B., Jung, K. W., McNab, A., Robertson, J., Skene, L. and Zoloth, L. (2007). Ethical standards for human-to-animal chimera experiments in stem cell research. Cell Stem Cell 1, 159-163.

Hyun, I. (2015). From naïve pluripotency to chimeras: a new ethical challenge. Development 142, 6-8.

Kobayashi, T., Yamaguchi, T., Hamanaka, S., Kato-Itoh, M., Yamazaki, Y., Ibata, M., Sato, H., Lee, Y.-S., Usui, J.-i., Knisely, A. S. et al. (2010). Generation of rat pancreas in mouse by interspecific blastocyst injection of pluripotent stem cellsCell 142, 787-799.

Kobayashi, T., Kato-Itoh, M. and Nakauchi, H. (2014). Targeted organ generation using MixI1-inducible mouse pluripotent stem cells in blastocyst complementation. Stem Cells Dev. (in press).

Lensch, M. W., Schlaeger, T. M., Zon, L. I. and Daley, G. Q. (2007). Teratoma formation assays with human embryonic stem cells: a rationale for one type of human-animal chimera. Cell Stem Cell 1, 253-258.

Matsunari, H. Nagashima, H.,Watanabe, M., Umeyama, K., Nakano, K., Nagaya, M., Kobayashi, T., Yamaguchi, T., Sumazaki, R., Herzenberg, L. A. et al. (2012). Blastocyst complementation generates exogenic pancreas in vivo in apancreatic cloned pigs. Proc. Natl. Acad. Sci. USA. 110, 4557-4562.

National Research Council (2005). Guidelines for Human Embryonic Stem Cell Research. Washington, DC: National Academies Press.

Rashid, T., Kobayashi, T. and Nakauchi, H. (2014). Revisiting the flight of icarus: making human organs from PSCs with large animal chimeras. Cell Stem Cell 15, 406-409.

Streiffer, R. (2010). Chimeras, moral status, and public policy: implications of the abortion debate for public policy on human/nonhuman chimera research. J. Law Med. Ethics 38, 238-250.

Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K. and Yamanaka, S. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872.

Thomson, J. A., Itskovitz-Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S. and Jones, J. M. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282, 1145-1147.

Usui, J.-I., Kobayashi, T., Yamaguchi, T., Knisely, A. S., Nishinakamura, R. and Nakauchi, H. (2012). Generation of kidney from pluripotent stem cells via blastocyst complementation. Am. J. Pathol. 180, 2417-2426.

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Of mice and men: exploring Mouse ENCODE

Posted by , on 17 December 2014

The Mouse ENCODE Project released a slew of papers late last month reporting findings from a three-year effort to comprehensively map functional elements in the mouse genome. Their major findings are summarized in an integrative paper in Nature (Yue, F. et. al., 2014). Similar to the goals of the human ENCODE project (The ENCODE Project Consortium, 2012 and the ENCODE portal), mouse ENCODE aimed to identify biochemically functional elements in order to better understand and design genomic and genetic studies in this important model organism (Mouse ENCODE Consoritum, et. al., 2012).
This isn’t the ENCODE groups’ first model organism — if you missed the fly and worm papers, they came out in January 2011 (The modENCODE Consortium, et. al, 2012; Gerstein, M.B. et al., 2012). The modENCODE Project had the similar goal of elucidating functional elements in these two important genetic systems. Mouse ENCODE does the same thing but with the advantage of much more closely matched tissue and cell types to human, with an eye to making mouse models of disease more genomically interpretable.
Methods/Data
The human effort emphasized their selection of cell lines or primary tissues to create the most versatile data resource: one with many experiments in a few select cell types, and a few very informative experiments across many (100s) of cell types. The mouse ENCODE Project organized themselves similarly, but can also take advantage of analyzing tissues over a range of developmental time points, an axis more difficult to study in human. In total the group generated over 1000 datasets spanning cells, tissues, and time points that go into the integrative analysis paper (Supplementary Table 1). Companion papers break down subsets of the data into more concentrated efforts to understand domains of replication timing (Pope, B.D. et. al., 2014), or regulatory and transcriptional conservation and divergence between human and mouse (Cheng, Y. et. al., 2014Sundaram, V. et al., 2014Stergachis, A.B. et. al., 2014, Lin, S. et. al., 2014).
Main points of paper
There have been many good overviews of the mouse ENCODE main integrative and companion papers since their publication in the Nov 20 issue of Nature (Carnici, P. 2014), and the authors of the integrative paper offer a bullet point summary of findings after the introduction. Here I will go into more detail on two sections of the paper: conservation of expression patterns and the conservation of cis-regulatory elements. My purpose  is to break down the high-level descriptions of methods that don’t get much space in the main text of the paper and to make accessible the usefulness of both methods and data in this seminal paper.
Expression patterns 
The field has been split on wether expression varies with tissue or is more closely tied to species, and there are data on both sides. Previous studies have found that expression is more tightly correlated with species; others find gene expression profiles between the same cell type in different species is more similar than different cell types in the same species. When Mouse ENCODE looked at expression of genes across many tissues and compared them to human, they found both are correct: there is evidence that gene expression is mostly conserved, but there is biological pathway-specific divergence. The principle component analysis in Fig 2a shows that overall gene expression tends to vary with tissue type, but that there is some variation due to species (principle component 2). Fig 2b pinpoints which genes vary more with species or cell type changes. Importance of this analysis is to reveal which genes/sets of (orthologous) genes are more species specific, and therefore may not be the best markers for disease model studies.
One major question in comparative genomics is if gene expression is conserved across species. The analysis so far suggests that yes, for some orthologs. To quantify this, the authors determine the conservation of co-expression using a novel method they call Neighborhood Analysis of Conserved Co-expression (NACC). The idea is to determine for a pair of orthologus genes if they have a similar correlation of expression with a set of “neighborhood genes” in each species. For a test gene X in human, the NACC method determines the Euclidean distance of the test gene to a set of “neighborhood genes” (also with orthologs in mouse). Then they quantify the same distance metric between the ortholog of test gene X in mouse and the orthologs of the neighborhood genes. The inverse analysis gives them two sets of Euclidean distances for each orthologous gene. Then the average change in both direction is a “symmetric measure of the degree of conservation of co-expression for each gene.” Fig 2c shows that orthologs tend to have more similar distances to their set of orthologous neighbor genes, quantified by a small deltaD (on the x-axis) compared to test genes randomly paired (not based on orthology). This suggests that most orthologous genes have conserved co-expression between species.
The authors can extend their NACC method to quantify correlation of any orthologous regions, for example, regulatory elements. They do this for H3K27ac peaks and DNaseI signal (Fig 4) and find that “most sequence alienable regulatory elements are conserved in activity”.
Cis-regulatory conservation and divergence
By sequence homology of regulatory elements (defined by chromatin mark data), Mouse ENCODE determines that between one-half to two-thirds of regulatory elements are conserved between human and mouse. Next they ask if divergent (species-specific) regulatory elements are enriched near genes for certain biological processes. This enrichment analysis reveals that mouse-specific regulatory elements tend to be located near genes for immune processes (Fig. 3c). This agrees with the conservation of co-expression analysis, which found that immune genes tend to have lower conservation of co-expression (Fig 2d). Together these data suggest that regulation of immune function in mouse is regulated distinctly from human.
If some processes, such as immune function, are regulated distinctly, how are those species-specific elements generated? They explore how elements may have been added or removed from the mouse genome by examining the overlap of enhancer elements with repetitive regions. 85% of mouse-specific enhancers overlap with a repeat element, more than expected by chance. Delving further, this enrichment is pronounced in specific subfamilies of mobile elements. Specifically, mouse-specific transcription factor binding sites are encroached in short interspersed elements (SINEs) and long terminal repeats (LTRs).
Contribution of mobile elements to gene regulatory networks has been a hypothesis in the field of gene regulation since Barbara McClintock (McClintock, B., 1956). The hypothesis has gained more evidence recently (see: Wang, T. et. al., 2007; Bourque, G. et. al., 2008; and Jacques, P. et. al., 2013). However, large-scale analysis of this hypothesis is enabled by advantages of longer sequencing technologies that can resolve repetitive regions and the abundance of data resources like the ENCODE Projects. The specific transcription factor enrichments across mobile elements in mouse is explored in more depth in Sundaram, V. et al., 2014.
Usefulness to developmental biology
The Mouse ENCODE goal of breaking down the genome into the functional parts should be very informative for the developmental biologist who wants to understand the regulatory structure of her favorite gene. The breadth and depth of sample types and assays means a biologist can visualize the chromatin structure of his/her gene(s) of interest in a relevant cell type or tissue.
To do this of course you’ll need to access the data. You can find it all through genome browser portals on the Mouse ENCODE website (mouseencode.org). You can also find the data hosted at the Wash U Epigenome Browser at epigenomebrowser.wustl.edu/browser.
Another aspect of the Mouse ENCODE work (and ENCODE in general) I’ve been thinking about is how these projects are improving our ability to predict functional elements with less information. In my mind this means three questions:
  • What are the criteria that tell us region a is X type of functional element?
  • How do we know if we have found all (or some % ) of X functional elements?
  • What is the most informative piece of data that can tell us if region b is X element vs Y element?
Most of these questions were addressed to a large extent in the ENCODE integrative paper published in 2012. In model organisms though, the more important metric is how to the identified functional elements relate to human and impact how we think about our models of human development and disease. A companion paper to the Mouse integrative paper starts to address this question (Cheng, Y. et. al., 2014). I encourage you to read it, but I can’t stop thinking about Figure 3c — images of mouse embryos  expressing a reporter construct of an identified functional element. The punchline is half of the reporters are tissue-specific and half are not — and the authors interpret this as “pleiotropic”.  What is unanswered is what is the defining feature that determines tissue-specificity vs. pleiotropy? That is what the developmental biologist wants to know so she can prioritize candidate regulatory elements to understand the molecular genetics of her developmental or disease process more precisely.
 
More companion papers
I’ve cited several throughout, but you can find a complete list of companion papers on the Mouse ENCODE publications webpage: http://mouseencode.org/publications.
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(Developmental) Biology around the internet- December 2014

Posted by , on 17 December 2014

Here is December’s round-up of some of the interesting content that we spotted around the internet!

 

News & Research:

– Masayo Takahashi was the winner of the 2014 Stem Cell Person of the Year award, while the STAP story was chosen as the Stem Cell Story of the Year, in an open vote in Paul Knoepfler’s blog.

– The Future of Research Symposium was organised by a group of postdocs who think that science needs to change. They reported in F1000 Research about this meeting and the outcome of their discussions.

– Nature featured an interesting article on how science in central and eastern europe has changed since the fall of the Berlin wall.

– Also in Nature, a look at the most cited papers of all time. Menawhile Altmetrics announced the most shared and talked about papers in the last year.

– An article in Business Insider discusses the Korean lab where you can clone your pet.

– The White House tells the story of some of the women who made important contributions to science.

Darwin’s notes on evolution have been released by Cambridge University.

– And The British Society for Cell Biology is running again their writing competition. The deadline for submissions is the 28th of February.

 

Weird & Wonderful:

– Ever wondered what to do with those old conference posters? Transform them into Christmas decorations!

– Working with flies? Then this Drosophila t-shirt is for you!

– The evolution of intellectual freedom in academia– by PhD comics

– Why did the germ cross the microscope? To get to the other slide! – a ‘good’ science joke found on twitter!

– And as part of their Advent calendar, the MPI-CBG in Dresden showed off the model organism coffee art served by their cafeteria

 

 

Beautiful & Interesting images:

– Great image of octopus eggs before hatching.

– For some great galleries of beautiful scientific images check out the winners of this year’s Olympus BioScapes competition, as well as 40 years of Nikon Small World competitions

– And in time for a sciency Christmas- a dissected gingerbread man!  


Videos worth watching:

– The winners of the Dance Your PhD Competition were announced!

 

 

 Keep up with this and other content, including all Node posts and deadlines of coming meetings and jobs, by following the Node on Twitter

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Looking inwards: opening a window onto human development

Posted by , on 16 December 2014

This editorial was first published in Development. It was written by Olivier Pourquié, Benoit Bruneau, Gordon Keller and Austin Smith.

 

The past 30 years or so have witnessed tremendous advances in the field of developmental biology. This has resulted in a growing (although still incomplete) understanding of the molecular basis of embryonic development, including characterization of signals and genes involved in establishing the embryonic axes and controlling organ development. This progress has been made possible largely thanks to a selected set of model organisms, including C. elegansDrosophila, zebrafish, Xenopus, chicken and mouse, chosen because they are particularly well suited for genetic and/or developmental studies. Large communities of scientists sharing common interests and tools have been built around these model organisms. The genomes of some of these model species were among the first to be sequenced, and huge amounts of data on each of these species have been organized into model organism databases, such as Flybase (www.flybase.org), ZFIN (www.zfin.org) or MGI (Mouse Genome Informatics; www.informatics.jax.org/).

One of the major realizations from the work of the past 30 years is the remarkable conservation of developmental processes between organisms as evolutionarily distant as flies and mice (the ancestors of which diverged over 600 million years ago). We now know that the set of genes found in animals is limited, in the range of 15,000- 25,000 (not counting alternative transcripts), and that essentially the same gene families are found across the entire animal kingdom. The same signaling pathways are repeatedly used during development of all species, and key genetic systems involved in patterning the body axis, such as the Hox genes, are also conserved. Moreover, many of the cellular processes that underlie morphogenesis and organogenesis are conserved. Much of this research has been published in the pages of Development.

Strikingly, although we understand intimate details of the development of a broad range of vertebrate and invertebrate species, we know almost nothing about the development of the human embryo beyond morphological descriptions. From these descriptions, it is clear that human development broadly resembles that of other mammals. Moreover, given the level of conservation of developmental processes at the genetic level, it seems highly likely that human development will also use the same palette of molecular tools. However – not unexpectedly, given the differences in size and life span – there are a number of important differences in the development of human and mouse embryos (Rossant, 2015). Studies of human development have been very limited, due to the highly restricted accessibility to human embryos. However, we now have the opportunity to study human development using stem cell differentiation as a surrogate. In vitro systems, based on the differentiation of pluripotent cells, strikingly recapitulate embryonic morphogenesis in a dish. This work was largely pioneered by Yoshiki Sasai, who showed first in mouse and then in human embryonic stem cell (ESC) cultures that they could self organize in vitro into structures as complex as a developing eye. This groundbreaking work opened the door to a series of studies demonstrating the possibility of differentiating other complex human neural structures, such as hypothalamus and even cerebral cortex, in vitro. Moreover, these self-organizing properties are neither restricted to pluripotent stem cells nor to ectodermal derivatives. As shown in seminal work by Hans Clevers and colleagues, endoderm-derived tissues, such as human intestine and stomach, can now be propagated as organoids and experimentally manipulated. The repertoire of tissues for which we now have three-dimensional (3D) in vitro models is growing rapidly, and it is likely that more human embryonic structures will soon become accessible using these approaches. This will undoubtedly constitute a major revolution for our field and open the door to the experimental study of human developmental biology. The deployment of sophisticated molecular and genetic tools already developed in model organisms will now be possible on these human organoids in an ethically acceptable context. Organoid culture might also provide a route to the generation of human tissues or even organs in vitro for regenerative medicine, whereas organoids derived from patients via either iPS cells or tissue stem cells will provide outstanding model systems to study the molecular basis of a broad range of pathologies and to identify and test drugs for various diseases.

In recognition of these recent breakthroughs and in line with Development’s recent expansion into the stem cell field, we organized the meeting ‘From Stem Cells to Human Development’ in September 2014, as part of The Company of Biologists workshop series. The meeting was a tremendous success, and those of us present had the impression of witnessing at first hand the emergence of this new field of human developmental biology. Many of the speakers were distinguished developmental biologists with a strong record of research using model organisms, but who had recently added human ESCs to their palette of model systems. One of the most striking aspects of the meeting was the recurring theme that, irrespective of the organ system, human ESCs differentiated in vitro can be coaxed to self-organize into organoids. These striking structures sufficiently resemble their normal in vivo counterparts to provide spectacular experimental systems for studying developing human tissues. We sorely missed Yoshiki Sasai, who had accepted to be the keynote speaker of the meeting but who tragically could not be with us (for a retrospective on his extraordinary career, see (Piccolo, 2014). In a fitting tribute, Austin Smith dedicated the meeting to his memory.

In this issue, you will find a report (Medvinsky and Livesey, 2015) on this meeting from two of the speakers – Alexander Medvinsky and Rick Livesey – as well as several Spotlight articles. Janet Rossant discusses key differences between early mouse and human development, and how these relate to the ability to derive different stem cell lines from these embryos (Rossant, 2015). Looking at much later stages of development, Hans-Willem Snoeck explains, using the lung as an example, why it is essential to understand human development if we are to make progress in treating disease (Snoeck, 2015). Although the potential of human stem cell research is immense, it does raise a number of important ethical issues, and Göran Hermerén and Insoo Hyun, who led a discussion session on ethics at the workshop, discuss some of the ethical considerations of working with human stem cells, with a particular focus on the ethics of generating human animal chimeras (Hermerén, 2015; Hyun, 2015). We hope you enjoy these contributions.

The human development field represents an essential growth area for the developmental biology community, and Development is keen to play an active role in supporting and inspiring it. The recent meeting was such a success, and the field is moving so rapidly, that we believe there is a need for further focused meetings in this area. We are therefore delighted to announce that we will be organizing a second meeting on the same topic in early 2016 – look out for further details in the coming months.We are also planning a Special Issue of the journal for Autumn 2015, focusing on human development (for more details, see http://dev.biologists.org/site/misc/HumanDev.xhtml). As much as Development has promoted research on model organisms over the past decades, we consider that a major new frontier lies in the emerging field of experimental investigations of human development, and we strongly encourage you to submit your work in this area.

 

Other articles in this issue focusing on human development:

Ethical considerations in chimera research, by Göran Hermerén

– From naïve pluripotency to chimeras: a new ethical challenge? by Insoo Hyun

– Mouse and human blastocyst-derived stem cells: vive les differences. by Janet Rossant

Modeling human lung development and disease using pluripotent stem cells, by Hans-Willem Snoeck

On human development: lessons from stem cell systems, by Medvinsky and Livesey

 

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In Development this week (Vol. 142, Issue 1)

Posted by , on 16 December 2014

Here are the highlights from the current issue of Development:

 

Planar cell polarity squeezes in on the action

FigureThe planar cell polarity (PCP) pathway regulates the polarization of epithelial tissues in various contexts, but recent studies suggest that the PCP pathway also influences other aspects of morphogenesis. Here, Sergei Sokol and colleagues uncover a role for PCP signalling during apical constriction in Xenopus embryos (p. 99). They show that the core PCP protein Vangl2 accumulates at the apical surface of blastopore bottle cells, which undergo apical constriction during gastrulation. The depletion of Vangl2 perturbs apical constriction and hence blastopore formation. The authors further demonstrate that Rab11, a marker of the recycling endosome, localizes to the apical surface of constricting cells in a Vangl2-dependent manner; apical staining of Rab11 is absent in Vangl2-depleted embryos, suggesting that PCP signalling modulates endocytic trafficking. Finally, the authors show that Rab11 in turn modulates Vangl2 distribution and that it cooperates with Myosin V to regulate apical constriction. Together, these studies highlight a novel role for the PCP pathway during apical constriction and support a positive-feedback model in which both PCP signalling and endocytic trafficking function to regulate apical constriction.

 

Epiblast development: getting up to speed

FigureThe epiblast of mammalian embryos undergoes a period of rapid growth shortly after implantation, thereby establishing a population of cells that will give rise to the embryo proper. Here, Miguel Ramalho-Santos and co-workers show that chromodomain helicase DNA-binding protein 1 (Chd1) is required for the transcriptional output that drives this rapid growth (p. 118). They first show that Chd1–/– mouse embryos display post-implantation defects; analyses of lineage and patterning markers indicate that Chd1–/–embryos arrest in the transition between E5.5 and E6.5, prior to anterior-posterior patterning and the onset of gastrulation. The researchers further show that transcriptional output per cell is reduced inChd1–/– mouse embryonic stem cells (ESCs) compared with control ESCs. In line with this, the amount of RNA polymerase II present at gene bodies and transcriptional start sites is decreased in mutant ESCs. Finally, the authors document that Chd1 also directly regulates the output of ribosomal RNA in both ESCs and the epiblast. In summary, the authors propose that Chd1 promotes a global increase in transcriptional output by both RNA polymerase I and II that, in turn, sustains the rapid growth of the epiblast.

 

Ezh2: balancing cell differentiation in the lung

FigureDuring development, the lung endoderm is patterned along its anterior-posterior axis, giving rise to distinct epithelial lineages, such as the alveolar cells that mediate gas exchange, and the basal and secretory cells that line the airways. In this issue (p. 108), Edward Morrisey and colleagues show that the polycomb repressive complex 2 component Ezh2 restricts the basal cell lineage during lung development, thereby allowing correct patterning of the lung. The researchers report that Ezh2 is broadly expressed in the lung during early development but then gradually becomes downregulated as development progresses. Importantly, they demonstrate that the endoderm-specific deletion of Ezh2 impairs secretory cell differentiation while inducing the ectopic and premature development of basal cells that express the transcription factor Trp63 and other basal cell markers. Furthermore, they report that Ezh2 deletion gives rise to a cell population that might represent an intermediate state between basal and secretory states. These and other findings indicate that Ezh2 controls the phenotypic switch between basal cells and secretory cells, and regulates both the temporal and spatial patterning of the lung.

 

MRTFs at the heart of epicardial motility

FigureThe epicardium – the single-cell layer of mesothelium that surrounds the heart – harbours a population of progenitor cells that modulates heart development and contributes to various cardiac lineages. During heart development, these epicardium-derived progenitor cells (EPDCs) undergo epithelial-to-mesenchymal transition and migrate into the sub-epicardial space, but the mechanisms regulating their mobilization remain unclear. On p. 21, Eric Small and colleagues show that myocardin-related transcription factors (MRTFs) regulate the motility of mouse EPDCs as well as the maturation of coronary vessels. They demonstrate that MRTF-A and MRTF-B are enriched within the epicardium, where they localize to the perinuclear space. The researchers further demonstrate that, in epicardial-mesothelial cells cultured in vitro, TGFβ signalling leads to the nuclear accumulation of MRTFs and the activation of a cell motility gene expression program. Importantly, the epicardial-specific ablation of Mrtfa and Mrtfb causes sub-epicardial haemorrhage; mutant hearts display a disorganised epicardial layer. In addition, lineage-tracing studies reveal a novel epicardial-derived coronary pericyte population that contributes to coronary vessel integrity and that is depleted in mutant embryos. Together, these findings, which link EPDC motility to cell differentiation in the heart, highlight novel approaches that could be used to manipulate EPDCs for cardiac repair.

 

Mga fuels pluripotent cells

FigureThe dual specificity T-box/bHLH-zipper transcription factor Mga is expressed in pluripotent cells of the mouse embryo and in embryonic stem cells (ESCs), but its function in these cells is unclear. Here, Virginia Papaioannou and colleagues examine the role of Mga in early development and show that it is essential for the survival of pluripotent cells (p. 31). They first show that Mga depletion in early mouse embryos and ESCs causes growth defects; increased cell death is observed in the inner cell mass (ICM) of mutant embryos in vivoand in vitro, and in Mga mutant ESCs cells in vitro. Lineage specification, in contrast, is unaffected by Mgadepletion. The researchers further identify the enzyme ornithine decarboxylase (ODC), which converts ornithine to putrescine in the polyamine synthesis pathway, as a candidate downstream target of Mga. Accordingly, they demonstrate that exogenous putrescine can rescue the ICM in Mga mutant embryos and the survival of Mga mutant ESCs. These findings highlight a role for polyamines in pluripotent cells and suggest that Mga controls cell survival in early embryos and ESCs by regulating polyamine pools.

 

Plus…

In recognition of recent breakthroughs and in line with Development’s recent expansion into the stem cell field, we recently organized a workshop – ‘From Stem Cells to Human Development’ – that was held in September 2014. In this issue, you will find a report from this meeting as well as an Editorial and several Spotlight articles that address key issues in this field.

Looking inwards: opening a window onto human development

Development Editors announce a new focus on human developmental biology and discuss how they hope to support this expanding field. See the Editorial on p. 1

Ethical considerations in chimera research

The use of human tissue, particularly in the generation of chimeric animals, throws up important ethical considerations that scientists and policy-makers must consider. See the Spotlight article by Göran Hermerén on p. 3

 

From naïve pluripotency to chimeras: a new ethical challenge?

The ability to create chimeric animal models using naïve human pluripotent stem cells is now on the horizon. Should we be concerned about using such chimeric animals? Insoo Hyun discusses these concerns on p. 6

Mouse and human blastocyst-derived stem cells: vive les differences

Early human and mouse embryos exhibit significant differences in their development and, as discussed by Janet Rossant, these are reflected in the properties of stem cell lines derived from these embryos. See the Spotlight on p. 9

 

Modeling human lung development and disease using pluripotent stem cells

Successful disease therapy often requires an in-depth knowledge of basic developmental biology, not only through study of model organisms but crucially also of human tissue. Hans-Willem Snoeck discusses the importance of using human stem cell models for understanding human lung development and disease. See the Spotlight on p. 13

 

On human development: lessons from stem cell systems

In September 2014, over 100 scientists from around the globe gathered at Wotton House near London for the Company of Biologists’ workshop ‘From Stem Cells to Human Development’. The workshop covered diverse aspects of human development, from the earliest stages of embryogenesis to differentiation of mature cell types of all three germ layers from pluripotent cells. , Here, Alexander Medvinsky and Frederick Livesey summarise some of the exciting data presented at the workshop and draw together the main themes that emerged. See the Meeting Review on p. 17

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Why Not Publish Your Antibody Validation Data

Posted by , on 15 December 2014

Antibodies are frequently used in developmental biology labs, but their validation is crucial to provide the information needed in order to reliably interpret the results of experiments. Antibody validation is also important to help scientists chose antibodies that will be suitable for their experiments, yet the results of these validations rarely get published.

To try and help F1000Research recently launched the Antibody Validation collection. Myself, along with my colleague Matt Helsby from Citeab and Mei Yeung from PeproTech EC Ltd are the guest editors of the collection which aims to provide a platform where researchers and companies can both publish their antibody validation studies regardless of the outcome, and look up existing validation articles for antibodies or experimental setups of their interest. Our goal is to enhance the reliability and reproducibility of antibodies in scientific research. Referees reviewing the validation studies will not focus on novelty and impact, but rather on whether the study is scientifically sound and provides all the relevant information. This allows us to publish validations which might otherwise be lost and include detailed methods and complete data (for example entire western blots).

Formal publication allows scientists doing these validations (which can be onerous and time consuming) to get some tangible credit for their efforts through a recognised citation which once peer reviewed, is indexed in PubMed. So, if you are using antibodies and you are regularly validating them, why not write up this data and publish it? By sharing your information you can help others receive valuable information about antibodies giving them more confidence in which ones they should use in their studies.

We want to be as inclusive as possible in this initiative and encourage participation from everyone involved in using, validating and manufacturing antibodies. So, if you have any thoughts on the collection or would like to be involved please let us know (research@f1000.com), as your suggestions/help will be most welcome.

Andy Chalmers (CiteAb/University of Bath)

 

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PhD position in developmental neurobiology- 2

Posted by , on 12 December 2014

Closing Date: 15 March 2021

How do carbohydrates instruct brain development?

APPLICATION DEADLINE 16th January 2015

Project Code:

2015-EastBio-001

The emergence of a brain at the front-end of a growing embryo requires very precise orchestration to make sure that the right structures form in the right place at the right times. Central to this process is not only the giving of instructions but also their proper transmission and reception.  Over the past few years scientists have made considerable strides  in identifying the protein signals, or ‘signalling proteins’, which transmit instructions between cells. Signalling proteins are produced by a source and move to their target where they are sensed by receptors on the surface of the target cell. The target cell then changes its behaviour in response to the signal.  A puzzling conundrum is that, despite intense efforts, only a relatively small number of signalling proteins have been identified compared to the complexity of instructions needed to produce the brain. We have focused our attention on the role played by a completely different class of molecules, the carbohydrates, in cell signalling. We are particularly interested in the idea that interactions between carbohydrates and proteins expand the diversity of instructions.

This project  will employ state-of-the-art confocal microscopy in combination with live cell imaging to look in detail at the interaction between biologically powerful signalling proteins called ‘morphogens’ and a structurally diverse type of carbohydrate called ‘Heparan sulphate’ (HS), a linear polysaccharide which is modified by differential sulphation. Morphogens are a class of signalling protein important for brain development as cells are very sensitive to the amount they encounter such that even small changes in level can have a dramatic effect on brain development including developmental defects. We have discovered that the pattern of HS sulphation regulates morphogen gradient emergence and signalling in the developing brain and that mouse mutants with abnormal HS structure have brain malformations (Conway et al., 2011; Clegg et al., 2014). In order to investigate the molecular mechanism in more detail, we are developing a novel culture system, which allows us to apply a source of morphogen labelled with green fluorescent protein (morphogen-GFP) to developing brain tissue and then track its movement over time. By comparing the behaviour of morphogen-GFP when presented with normal and abnormal HS we can build up a picture of how HS normally functions and how the process can go awry. The overarching goal of the project is a deeper understanding of how carbohydrates and proteins coordinate to instruct biological processes.

This project will provide training in advanced confocal microscopy and image analysis as well as more standard molecular biology techniques involved in building GFP expression constructs, gene expression analysis, and working with transgenic mice. Live cell imaging is an area of rapidly-growing importance in both academia and commercial environments, because only this technology delivers results with high temporal and spatial resolution of molecular events such as the in vivo distribution of morphogens etc. The skills acquired will be of great value and transferrable to many other research areas, either in academia or the biotechnology / pharmaceutical sector.

This project is part of the BBRSC EASTBIO Doctoral Training Partnership. For information on this scheme please see http://www.eastscotbiodtp.ac.uk/

References
Clegg, J. M., Conway, C. D., Howe, K. M., Price, D. J., Mason, J. O., Turnbull, J. E., Basson, M. A. and Pratt, T. (2014) ‘Heparan sulfotransferases hs6st1 and hs2st keep erk in check for mouse corpus callosum development’, The Journal of neuroscience 34(6): 2389-401.

Conway, C. D., Howe, K. M., Nettleton, N. K., Price, D. J., Mason, J. O. and Pratt, T. (2011) ‘Heparan sulfate sugar modifications mediate the functions of slits and other factors needed for mouse forebrain commissure development’, The Journal of neuroscience 31(6): 1955-70.

 

Additional Project Info:

This project is part of the BBSRC EASTBIO Doctoral Training Partnership and applications will be directed to this programme.
To apply for this PhD  position please visit the Edinburgh Neuroscience PhD Gateway
http://www.edneurophd.ed.ac.uk/development-neurones-and-networks/how-do-carbohydrates-instruct-brain-development%232015-eastbio-001
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PhD position in developmental neurobiology- 1

Posted by , on 12 December 2014

Closing Date: 15 March 2021

Functional importance of HS carbohydrates in brain development.

APPLICATION DEADLINE 5th January 2015

Project Code:

2015-CIP-012

Understanding the developmental mechanisms which create the CNS of healthy individuals is important for understanding neurological and psychiatric disorders with neurodevelopmental components. Although great strides have been made in identifying key regulators of this process our understanding is still rudimentary. Improving our knowledge base in this area is likely to impact on future attempts to understand disease and regenerate damaged circuitry.

While the roles played in signalling by proteins, secreted ligands and their receptors as well as transcription factors, has been intensively studied the roles played by carbohydates, while generally acknowledged as important, have been under-explored. Our research focuses on a class of membrane-associated and extracellular molecules called heparan sulphate proteoglycans (HSPGs) and more specifically on their carbohydrate component heparan sulphate (HS). HS interacts with signalling molecules critical for development so is well placed to coordinate developmental programs.  The permutations of HS structural modification, largely as a result of differential sulphation, are so numerous that HS has the potential to be the most information-rich biopolymer known, making it an excellent candidate for regulating complex events involved in brain development and an important molecular system to understand.

The corpus callosum is a well studied model system for the development of complex neural structures and connectivity so is ideal for investigating the function of novel signalling molecules such as HS. We have identified HS modifying enzymes which are essential for normal callosal development proving the functional importance of differential HS sulphation in this sysyem (Conway et al., 2011; Clegg et al., 2014). We are now well placed to take this work to the next level and investigate the underlying cellular and molecular functions of the hitherto relatively unexplored HS molecule.

This project will explore how the controlled regulation of differential HS sulphation by HS modifying enzymes is an essential component of brain development. The project will use transgenic mouse, ex vivo culture, and/or imaging approaches to obtain a deeper understanding of the normal cellular and molecular functions of HS in the developing mammalian brain.

 

References:

Clegg, J. M., Conway, C. D., Howe, K. M., Price, D. J., Mason, J. O., Turnbull, J. E., Basson, M. A.and Pratt, T. (2014) Heparan sulfotransferases Hs6st1 and Hs2st keep erk in check for mouse corpus callosum development, J Neurosci 34: 2389-401.

 

Conway CD, Howe KM, Nettleton NK, Price DJ, Mason JO, Pratt T. (2011) Heparan sulfate sugar modifications mediate the functions of slits and other factors needed for mouse forebrain commissure development. J Neurosci. 31:1955-70.

 

Pratt lab page

http://www.ed.ac.uk/schools-departments/integrative-physiology/staff-profiles/tom-pratt

 

To apply for this PhD position please go to the Edinburgh Neuroscience PhD gateway page

http://www.edneurophd.ed.ac.uk/development-genetics/functional-importance-hs-carbohydrates-brain-development%232015-cip-012

 

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Two Postdoc scholarships in Cancer Biology

Posted by , on 11 December 2014

Closing Date: 15 March 2021

Two Postdoc scholarships in Cancer Biology

with focus on the EMT process

at Umeå Centre for Molecular Medicine

http://www.umu.se/english/about-umu/news-events/grants/12-1803-14

 

Umeå Centre for Molecular Medicine (UCMM) (www.ucmm.umu.se) is an interdisciplinary research centre with several research groups that study areas of biological and medical relevance. Localized in a tight environment of diverse biomedical laboratories, UCMM forms a creative and interactive unit for cutting edge biomedical research.

 

The scholarships are for 1 year with the possibility for 1 year extension.

Starting date: As soon as possible

Project description

The main focus is to understand the molecular mechanisms that control the epithelial-to-mesenchymal-transition (EMT) process. The project will initially use developmental biology processes as model systems to study EMT, with the possibility to validate our results in established in vitro and in vivo cancer models. The applicants will use functional experiments such as cell and tissue cultures, as well as chick in ovo electroporations and analysing relevant mice mutants. The studies involve common developmental and molecular biology methods like; immunohistochemistry, in situ hybridization, and statistical analyses and image preparations.

Qualifications

The ideal candidates should be PhDs with a background in cancer, molecular or developmental biology, and passed an animal research course. A thorough theoretical and practical grounding in molecular and cell biology is a prerequisite. Practical experience with functional cancer (EMT) models, vertebrate embryonic model systems, molecular and cell biology methods and live imaging is an advantage. The applicants should be proficient in written and spoken English, and have good computer skills (Word, Photoshop, Excel). Of importance are also good organizational, independence, cooperation and problem solving skills.

Other qualifications

An international postdoctoral training in the field of Cancer Biology, Molecular Biology or Developmental Biology is a merit.

 

For further information please contact: Professor Lena Gunhaga, 090-785 44 35, lena.gunhaga@umu.se

 

Applications that are submitted electronically should consist of a single document in Word or PDF format and include the following information; 1) The applicants research interest, experience and suitability for the scholarship

(max 1 page).

2) Methods that the applicant master (max 1 page).

3) Curriculum Vitae of the applicant including publication list.

4) Names and contact information of 2 referees, and stated professional

relationship with the applicant (max 1 page).

 

Your complete application marked with reference numberFS 2.1.12-1803-14, should be sent to medel@diarie.umu.se to be received by 8 of February, 2015, at the latest.

We look forward to receiving your application!

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