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Post-doctoral position in pancreatic tissue engineering available in the Spagnoli lab. at King’s College London

Posted by , on 12 February 2019

Closing Date: 15 March 2021

A Postdoctoral Research Associate position is available in the Spagnoli lab. in the Centre for Stem Cell and Regenerative Medicine at King’s College London. The candidate will work on an exciting EU-funded FET-Open consortium to bioengineer pancreatic tissue (https://www.pan3dp-project.eu/).

The Spagnoli lab (https://www.spagnolilab.org/) studies the mechanisms regulating cell identity and plasticity of metabolic organs, such as the pancreas and the liver. We use a combination of genetic approaches with genomic strategies and imaging in mouse embryos and human stem cells to study how distinct cell types, such as liver and pancreas, arise from common progenitors and acquire specialized shape to form functional organs.

The lab. is coordinating a multi-disciplinary FET European consortium with the ambitious goal of developing an innovative bio-engineering approach for generating pancreatic tissue. Tissues and organs comprise multiple cell types with specific biological functions that must be recapitulated in engineered tissue. We will biomimic developmental processes to fabricate 3D pancreatic tissue units that allow sustained cell viability, expansion and functional differentiation ex vivo.

This position seeks a highly motivated and creative individual with a strong interest in developmental biology. The candidate will be primarily responsible for establishing a 3D-imaging and transcriptome atlas of pancreatic cells and defining cellular sources for engineering pancreatic tissue units. This is a highly collaborative project, in which the successful candidate will work closely to all members of our team and participants of the interdisciplinary FET consortium.

The Centre for Stem Cells & Regenerative Medicine (CSCRM) at King’s College London acts as the nucleus for a vibrant and collaborative stem cell research community, being an ideal environment for a successful postdoc experience.

Qualifications:

Applicants should have a recent Ph.D. degree or M.D./Ph.D. degree. Candidates with experience in stem cell and developmental biology, confocal microscopy, image acquisition and analysis will be preferred.

Requirements:

A CV and a statement of research interests along with names of 2 referees should be sent via online application (see below).

Contact:

francesca.spagnoli@kcl.ac.uk

https://www.spagnolilab.org/

https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/stemcells/people/dr-francesca-spagnoli.aspx

 

If you are interested in applying for this role, please apply via our King’s College London link below:

https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1&p_internal_external=E&p_display_in_irish=N&p_process_type=&p_applicant_no=&p_form_profile_detail=&p_display_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=009906

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Postdoc position in zebrafish genetics and imaging

Posted by , on 11 February 2019

Closing Date: 15 March 2021

We seek an outstanding postdoctoral candidate to join the Yeh Laboratory at Texas A&M University in College Station (http://biomed.tamu.edu/tml).  Our group uses interdisciplinary and quantitative approaches to study the molecular and cellular basis of embryonic development, with specific focus on brain development.  In this context, we are interested in understanding how complex multi-enhancer regulatory landscapes interact with gene promoters through the application of super-resolution, live cell imaging.  A particular strength of the lab is the development of custom, state-of-the-art microscopy systems for applications in the life sciences.

 

The candidate will be independent, creative, motivated, and able to work collaboratively with a group of researchers with expertise in microscopy, physics, and developmental biology.  A PhD in the biological sciences (or related fields) with at least 3 years of laboratory research experience in zebrafish developmental biology is required.  Experience with quantitative imaging, in addition to experience in zebrafish development, will be considered positively, but is not required.

 

This is a renewable, two-year position with full benefits, based upon good performance of the candidate and availability of funds.  Salary will be competitive and dependent on the level of experience of the candidate.  Applications submitted before March 8, 2019, will receive full consideration, but the position will remain open until filled.

 

Applicants should provide,

  • cover letter describing research interests and career goals,
  • CV,
  • letters of recommendation from at least two references.

 

Submit applications to Alvin Yeh, ayeh@tamu.edu

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François Jacob Conference:

Posted by , on 11 February 2019

François Jacob Conference: Evolution, Structure and Function of Chromosomes High Order Structure

Institut Pasteur, Paris
June 4 (2pm) –June 7 (6pm) 2019

http://www.hic2019.conferences-pasteur.org/

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Postdoctoral Fellowship in Vascular Development at Washington University

Posted by , on 10 February 2019

Closing Date: 15 March 2021

Postdoctoral Fellowship in Vascular Development at Washington University 

Seeking applicants for postdoctoral fellowship positions in the lab of Dr. Amber Stratman at Washington University in St. Louis, Department of Cell Biology and Physiology.  The laboratory takes a multimodal approach to studying vascular development utilizing zebrafish, specialized 3-dimensional in vitro assays, and genomics to identify pathways modulating blood vessel formation, patterning, and stabilization.  Particular strengths of the lab focus on mural cell biology, vascular hemorrhage, and blood flow mediated gene regulation.  Opportunities to compete for external funding are highly encouraged.

 

Candidates with a PhD or MD/PhD in Molecular Biology, Cell Biology, Physiology, or related fields are encouraged to apply.  Interested candidates should provide a single file containing a cover letter (describing their research experience and future interests), a CV, and contact information for three references to Dr. Amber Stratman (a.stratman@wustl.edu).

 

Additional information available upon request.

 

Required Skills:

-MD/PhD or PhD in Vascular Biology, Molecular Biology, Cell Biology, Physiology, or related fields

 

Preferred Skills:

-Experience with tissue culture and molecular biology techniques

-Experience working with zebrafish

-Ability to work independently, yet maintain open communication with peers

-Sound verbal and written communication skills

 

http://dbbs.wustl.edu/faculty/Pages/faculty_bio.aspx?SID=6782

http://cellbiology.wustl.edu/stratman_a

 

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CRISPR babies: a view from the centre of the storm

Posted by , on 8 February 2019

This article by Robin Lovell-Badge, published this week in Development, gives a front-row view of the CRISPR babies scandal from last year. When the story broke, we collated reactions from the field – be sure to check them out too


Towards the end of November 2018, news broke that the Chinese researcher He Jiankui had created the world’s first genome-edited babies. This came shortly before the start of the Second International Summit on Human Genome Editing, where researchers, ethicists and others concerned with regulation, social issues and public engagement from around the world gathered to discuss the latest advances in the field. In this Spotlight, I provide my perspective on the events that occurred shortly prior to and at the summit, where He Jiankui gave an account of his activities. I also discuss what was wrong with his approach and how, after more research and with appropriate regulation, clinical applications of germline genome editing in humans may be justifiable.

 

Matt Porteus (right) and Robin Lovell-Badge (left) taking the opportunity to clarify some of the statements made by He Jiankui in his presentation at the summit, before opening up to questions from the audience. Courtesy of Vivian Tam (School of Biomedical Sciences, University of Hong Kong).

 

A month or so before the Second International Summit on Human Genome Editing took place, several of us on the organising committee heard rumours that He Jiankui (Southern University of Science and Technology, Shenzhen, China; who I’ll refer to as JK) was using genome-editing techniques on human embryos for the purposes of trying to make children who would be resistant to infection by HIV. We knew that JK had presented relevant work, involving genome editing in mouse and monkey embryos, at meetings over the last couple of years, and that he had also started using the methods on human embryonic stem cells and human embryos in culture. However, there was concern that he felt he was in a position to try things for real: to make genome-edited human babies. We also heard rumours that JK had obtained local ethics committee approval to go ahead. Therefore, when we were deciding on additional speakers for the summit, JK’s name came up. Although we were aware that he had not published in this area, he had clearly been doing relevant research and we thought it might be useful for him to attend the summit where the science, safety, ethics and regulatory issues surrounding genome editing would be discussed. We sent him an invitation and he responded almost immediately to say that he would be very happy to present. As moderator of the session he was going to be in, I had a conference call with JK and other speakers shortly before the summit. In advance of that call, JK sent me a draft summary of his talk. The summary highlighted the areas he was going to cover, including some preclinical data, but it certainly did not mention that he had edited human embryos and implanted them.

Late afternoon on Sunday 25 November, 2 days before the summit was due to begin, I was contacted by one of the staff members from the US National Academies of Sciences (NAS) who was coordinating the organising committee, asking if I could meet urgently. She had received a message from Jennifer Doudna (University of California, Berkeley, USA) who had just heard directly from JK by e-mail that two babies had been born following genome editing of early embryos. There were only a few details available at this point, but it was clear that the story was about to break in the press. Indeed, later that night an article was published by MIT Technology Review, which reported that JK had indeed created ‘CRISPR babies’. It turns out that their journalist had been in China, had heard rumours of what JK was up to and had managed to find clinical trial documents that JK had posted. After a little more digging, this journalist and the MIT Technology Review presumably took the decision to publish the story shortly before the summit started. It also turned out that JK had been using the services of a PR advisor who suggested that JK should have a journalist from Associated Press (AP) document his work and make videos to explain his research, so that he could make a big splash when the story was eventually released. Apparently, JK had submitted a manuscript to a ‘top journal’ and wanted to wait for the paper to come out before releasing the videos; he stated that it was not his intention for the story to be announced just before the summit. However, once it was clear the MIT Technology Review piece was coming out, AP needed to release the details that they had gathered, or they would lose their ‘scoop’. JK must have also decided, or been (ill-)advised by his PR consultant, to release the videos.

We obviously then needed to decide what we were going to do about all of this. More members of the committee arrived early Monday morning and we collectively took the decision that, assuming JK was still willing to talk, he should be encouraged to present at the summit. We subsequently received some criticism for this – about giving him a platform – but we stuck with our original decision because it was the only way of getting the story out in public, allowing JK to explain what he had done and why.

Jennifer Doudna and I met JK briefly on the Monday morning to get some confirmation from him about the stories that were already developing in the media. This was critical because I was due to attend a pre-summit press briefing, along with David Baltimore of the NAS, Lap Chee Tsui of the Hong Kong Academy of Sciences and Patrick Tam (University of Sydney, Australia) – another member of the organising committee who is fluent in Cantonese – and it was obvious that the main topic of questioning would be about what JK had done. We also wanted to stress to JK that he should take the opportunity to present the story in full at the summit in the Wednesday morning session. Jennifer and I also arranged to meet him that evening over dinner.

The questions in the press briefing were indeed very much focused on JK and his activities. This was a pity since the summit was going to cover many other topics of importance, including new developments in understanding the science of genome editing, uses of editing methods for somatic gene therapy, how ethical and public views had evolved over the past few years, and the different approaches to regulation according to culture and country.

That evening, Jennifer, myself and JK were joined by a few other committee members, including Alta Charo (University of Wisconsin-Madison, USA) and Matt Porteus (Stanford University, CA, USA). JK had brought his laptop to show his data. As he explained what he’d done, we were increasingly horrified, while JK was getting more and more anxious, in part because we were challenging him, but also because he had apparently started to receive threats and was nervous the press would find him. He left, having checked out of the hotel where all of the speakers were staying, and moved to a different, undisclosed hotel. I maintained contact with JK via e-mail and continued to encourage him to speak at the summit, and we discussed the arrangements we were prepared to make for him. This involved splitting the session he was in to allow the first four speakers to have a separate Q&A session before JK’s talk. Of course, we also had to take special security measures. He disclosed his location to Hong Kong University security, who brought him to the venue, where he was to wait in a hidden room until I called for him to give his presentation. We knew there were going to be many journalists attending – indeed there were about 160 corralled into one section of the auditorium – and that they would have many questions. To prevent an unruly Q&A session, we asked the journalists to write their questions out in advance. I also had permission to close the session if the media or other audience members misbehaved, and I warned everyone of this, both at the start of the session and just before JK’s talk.

As with the rest of the summit, the first four talks of the session were excellent and stimulated some good discussion. However, everyone was anticipating JK’s talk. There was a nervous wait between my calling him to come on to the stage and his appearance, and then we couldn’t hear anything because the cameras were going off continuously. I had to ask the photographers to stop before things quietened down enough for JK to give his talk. Matt Porteus then joined us on the stage and the two of us questioned him to ensure we all had the full story. This is when it transpired that there was a second woman with an early pregnancy from a genome-edited embryo, and that JK himself had taken the consent from the ‘patients’ (the prospective parents), which is against standard practice in experimental clinical practice. David Baltimore, the chair of the organising committee, then made a personal statement, relating his views – essentially his horror and dismay at what he had just heard –before I took questions from the audience and read selected ones from the media. The whole idea was to get JK to talk, because we knew that this would be the only opportunity that most people would have of interacting with him. The questions were often challenging and the answers sometimes evasive, sometimes direct, but all revealed how much JK had thought his work important, but how little he matched normal standards of evidence and clinical practice.

 

JK was whisked away by the security team immediately after the session, but hungry journalists needed someone to answer their many questions. Courtesy of Vivian Tam (School of Biomedical Sciences, University of Hong Kong).

JK did not want to face the media after the session and was whisked away by the security team. He returned fairly promptly to Shenzhen, where he lives, although he was rapidly barred from his university, who deny knowledge of his activities. There is now an official investigation into what JK has done, and how he managed to evade proper oversight. He is apparently not under arrest, but he is being guarded and it is likely that his movements are restricted.

So, what do we know about the study itself? We know that JK submitted a paper(s) to a journal, but it is doubtful that the study meets the (or any) journal’s requirements concerning ethics approval, consent, etc. The hospital referred to in some of the clinical trial documents denies knowing about the work, although it is possible this might be to protect the identity of the families concerned. The latter was something JK stressed was important, but he clearly had not thought through very carefully what would happen to them when the story broke. We also know that there were eight couples enrolled in the trial, but that one dropped out. In total, many embryos have been manipulated, cultured, subjected to preimplantation genetic diagnosis (PGD) and then frozen. We don’t know how many attempts have been made at transferring them. All we know is that two embryos from one couple were implanted, which resulted in the twin baby girls (known as ‘Lulu’ and ‘Nana’), and that another embryo transfer has led to an ‘early stage pregnancy’. It is clear that JK, who is a physicist by training, had been building up to do this for quite some time, but he clearly bypassed the normal practices of science and clinical practice. He apparently did talk to a few experts on genome editing, but ignored their advice, and should have talked to more. He did not properly consider the risks of using genome-editing techniques in human embryos; indeed, he ignored evidence indicating incorrect on-target alterations, off-target events and mosaicism in the embryos that were implanted. Moreover, JK did not give adequate thought to the gene he was targeting. CCR5 is clearly an interesting gene. It is the subject of the first somatic genome-editing clinical trial for treating patients with HIV/AIDS. There are millions of people who naturally have mutations in CCR5, the most common being the delta-32 mutation, which is thought to have arisen in Northern Europe and confers resistance to HIV/AIDs. Perhaps that is why JK thought that making babies with this mutation would be fine. But he clearly hadn’t read widely enough or thought deeply enough about the consequences. There are almost no people with the delta-32 mutation living in China (Jiang et al., 1993). Therefore, it is necessary to ask ‘why?’ Perhaps the mutation simply has not spread this far. Or is it because carrying this CCR5 mutation might also confer susceptibility to something else? It is already known that it makes individuals more sensitive to Western Nile virus. There are also claims that it can make people more sensitive to the bad effects of influenza, although there are also reports suggesting that it does not (e.g. Matos et al., 2019). These studies deal with relatively low numbers of individuals in different countries, before or after recent pandemics may have skewed results, making it difficult to come to any conclusion, and certainly not with respect to the consequences of mutating CCR5 in individuals of Chinese origin. Some papers published a while ago do report other different specific CCR5 mutations in China (Ansari-Lari et al., 1997; Shioda et al., 2001), with some in vitro evidence suggesting weak HIV resistance, but there does not seem to have been any follow-up studies to confirm this. JK may have been aware of this research, but went ahead anyway, without judging that more needs to be done to provide concrete data. It has also been reported that decreased CCR5 activity can improve cognitive function in mice (Zhou et al., 2016). Of course, mice and humans are very different, but this raises the issue of whether mutating CCR5 might actually ‘enhance’ individuals rather than just making them resistant to a virus. Again, JK said publicly that he was aware of this study, but he ignored it.

 

He clearly bypassed the normal practices of science and clinical practice.

 

JK’s rationale was clearly to make children resistant to HIV. Apparently, there is a lot of stigma associated with being HIV-positive in China, or even having a family member who is, and children with HIV-positive parents are often ostracized. This may sound like an acceptable reason, but dealing with the social issues should really be a priority. Moreover, if the father is HIV-positive, as in this case, there are already methods to prevent HIV transmission to children that work extremely well. These involve first ensuring that the viral load is low by providing anti-viral drugs, and then washing the sperm prior to IVF. There was, therefore, no compelling reason or unmet need to use germline genome editing of CCR5.

The genome-editing technology itself is, in most people’s opinion, not yet ready for use, but this is also something that was overlooked by JK. It is clear that both babies are mosaic for the edits, i.e. not all their cells contain them. This happens when the edits occur in the late one-cell embryo or even at the two-cell stage, and current research seeks to develop methods to avoid this inefficiency. While off-target events don’t seem to be as much of a concern now, there are still issues with on-target events not being necessarily what you want. JK used simple non-homology end joining (NHEJ) to make small mutations. Initially, he told us that he was trying to recreate the delta-32 mutation but that this hadn’t worked in one of the babies. In fact, what we know now is that it had not worked at all: none of the embryos he implanted contained delta-32 mutations. They harbour completely novel mutations, of which we have absolutely no understanding. They may fail to confer HIV-resistance and could even lead to deleterious effects on the immune system or the brain. There was no preclinical data to assess the consequences of the specific mutations engineered by JK in the embryos before they were transferred in to the mothers. All this shows that JK didn’t know enough about CCR5 or the potential risks of tinkering with this gene. Of course, we could now recreate those mutations in mice or other animals and determine their effects. In theory, it would also be possible to take blood samples from Lulu and Nana when they are older and see whether their white cells are resistant to HIV. However, it’s not going to be easy to fully understand the effects of the mutations he made. The role of CCR5 in the brain is poorly understood, and it will not be simple to test the consequences of the mutations made, on either HIV resistance or CNS function. Nor will it be trivial to assess whether such genome-edited individuals are more prone to the serious effects of influenza, etc.

JK had not published any of his preclinical data, raising some doubt that he was competent to carry out what he has claimed, but in failing to do so he has given the impression that he wanted to conduct the work in secret. Of course, this also means he has failed to benefit from the critical process of peer-review. He obviously hadn’t taken sufficient advice to understand the best way of going about doing a very novel, clinical procedure. He also seems to have assumed he knew best when it came to the ethics of what he was doing and the way to obtain consent from the parents, when in reality this fell far short of normal practice, with JK conducting much of this himself, apparently with his ex-mentor Michael Deem (from Rice University, Houston, TX, USA), another physicist. He also did not talk to the relevant regulators to seek their approval. Yet he did seem to be aware of the regulations; however, when challenged, he argued that they were guidelines – they weren’t laws – and that they were drawn up with respect to stem cell research and were not relevant to what he had done. Naturally, there was quite a lot of discussion at the summit about whether or not what he did was illegal. We will have to wait and see exactly what happens, but most commentators in China say that he has directly contravened laws, although it is unclear whether there are any penalties prescribed for doing so.

So why did JK do this? I think that he honestly thought he was doing a good thing and that everyone would realise this. He seems a driven and ambitious person, who had had success in his work on genome-sequencing technologies, and he wanted to be the first to carry out germline genome editing. He told us that his hero was Bob Edwards, who pioneered IVF, and that he thought it was amazing how many babies have been born through this approach. JK thought germline genome editing would be the next big thing and wanted to emulate his hero. However, Edwards published all the experimental and preclinical work that led up to the first successful application of IVF, and subsequent research. Other scientists, clinicians and the relevant authorities knew what Edwards was doing and why. There weren’t specific regulations at the time, and there probably had not been much public dialogue beforehand, something that has subsequently become important, but Edwards didn’t do anything against people’s expectations, and his intentions were not just clear, they were open. In contrast, JK failed to do any of this.

JK’s rationale for doing what he claims was to try to make children resistant to HIV. Some have argued that this is a form of enhancement, and that this is wrong in itself. However, it is not as simple as that. Vaccines give people disease resistance and their use is not only widely accepted, it is encouraged. However, JK did not properly take into account the risks of editing CCR5, and the way that he did this, versus any benefit. Making novel genetic alterations, especially in a gene whose normal function is not sufficiently well understood, poses lots of risks, and of course there are risks to the children if their identity becomes known. Moreover, all these risks are unnecessary since, as mentioned above, there was no clinical need or benefit for the genome editing in this case. But are there instances in which genome-editing human embryos might be beneficial? In my opinion, there are. For instance, there are cases in which one parent is homozygous for a dominant disease-causing mutation – an obvious case is Huntington’s disease. Although this is very rare overall, there are clusters of individuals where this happens, and thus cases where such diseases have blighted families for generations. There are also rare instances where both parents are homozygous for a recessive deleterious variant of a gene and, again, it is not possible for them to have children that aren’t affected. In the case of heterozygote parents, PGD following IVF can be used to select embryos that aren’t affected. But while PGD sounds straightforward – it involves testing for the presence of the abnormal and normal allele in a biopsy of a few cells taken from each preimplantation embryo after IVF, and only implanting those that are disease free – there are lots of complications associated with this approach. It is necessary to find an embryo that is going to be free from the disease, but that is also good enough quality to give you a child, and that’s often a challenge, especially if the number of embryos obtained is low, which happens all too often. Some genetic diseases affect fertility, adding to the problem. A recent paper that evaluated data on PGD showed that a surprisingly large number of families never got the child they wanted because it was just too inefficient (Steffann et al., 2018). And that’s just if you’re screening the embryos for one gene variant. If you have to do two or more, it becomes really difficult to find an appropriate embryo to transfer. This is the case for ‘saviour’ siblings, where a couple already have one child, but that child has developed leukaemia, and they want to have a second child anyway in order to use bone marrow from the second child to rescue the first. Indeed, in a recent programme conducted at Harvard Medical School involving eight families, each woman went through, on average, five cycles of IVF, which is a lot, but only one baby was born who could be a saviour sibling. By using genome editing to correct the mutation leading to leukaemia, and by just carrying out the screening for tissue typing, it may have been possible to have helped all of those families.

 

But are there instances in which genome-editing human embryos might be beneficial? In my opinion, there are.

 

We also need to be aware that, as somatic gene therapy and conventional treatments improve, we are going to reach a situation where many more individuals suffering a genetic disease will survive to reproductive ages. They may want to have their own genetically related children, but without passing on probably even one deleterious allele to their children. Duchenne Muscular Dystrophy, for example, is an interesting case. Very few boys with this survive to reproductive age. However, if somatic gene editing works, those boys will now have the gene corrected in the relevant somatic cells but not in their germline. They might feel that embryo genome editing could give them the chance to overcome this and have children of their own that are unaffected and also not burden future generations with the need to undergo PGD or be fearful of having children. Overall, I think there is a medical need for genome editing in human embryos, a conclusion reached by the US National Institutes of Sciences’ and the Nuffield Council’s reports on human genome editing and by other organisations.

Although it is still too early to begin clinical trials, I think it would actually be irresponsible for us not to explore this opportunity further. We need to do the basic research, determine exactly what we can and can’t do, and work out whether we can really make genome editing efficient and safe enough to use in human embryos. The science is progressing fast, and new methods look very promising. The newly developed approach of base editing, for example, may be much safer than other approaches because it doesn’t involve a double-strand DNA break and hence avoids NHEJ-induced inappropriate on-target deletions or insertions. Off-target effects can be minimised by careful design of guide RNAs and through introducing the genome-editing components to minimise the period during which they can act. In fact, evidence now suggests that off-target effects are very rare. For example, work from my colleague Kathy Niakan (Francis Crick Institute, London, UK) revealed some on-target problems, but no off-target events (Fogarty et al., 2017). Shoukhrat Mitalipov (OHSU, Portland, OR, USA) also used genome editing in human embryos and did not observe off-target events (Ma et al., 2017, 2018). Even in JK’s study, the PGD analysis suggested that while there might have been an off-target event in one embryo, when they analysed DNA from the babies at birth this had disappeared. But of course, we have not seen all the data and how it was generated; there could be additional off-target events of which JK is unaware.

Assuming we can get to a point where the editing is efficient and safe, we clearly need to make sure it is used appropriately. Indeed, in the NAS report on Human Genome Editing (published in February 2017), we set out various guidelines, conditions and principles that should be considered when editing the human genome. These clearly weren’t enough to stop JK, so there have been, of course, calls for a moratorium. But I don’t think this would serve any purpose. How do we enforce one? Should this be just a temporary pause? For how long? What conditions would need to be met before we could lift the moratorium? Would a moratorium have stopped JK? I don’t think it would have. Moreover, to achieve a moratorium you would have to have consensus from all countries, which is again extremely unlikely. Therefore, I think it’s more a question of coming up with better guidelines. This would have to be carried out in a much more detailed way than has been the case to date. We clearly need to set out the minimal conditions that would have to be met with respect to a variety of issues: the scientific and clinical issues surrounding the gene that is being modified; the types of alleles that are being altered; the clinical need for the suggested alteration; and the efficiency, accuracy and safety of the proposed techniques (in terms of off-target events, on-target events, mosaicism, etc.). We should also establish the minimum requirements in terms of preclinical data (e.g. experiments in animals, human stem cells and perhaps in human embryos in vitro) and ask that they should be published. Processes for obtaining consent and ethical review approval should also be spelled out. Finally, we should also detail how the patients would be looked after and tracked, how we could actually diagnose what has happened in the embryos, how long-term follow up studies would be reported, and how patient protection and privacy will be considered. It has been suggested that this call for such a detailed translational pathway might encourage clinical applications and potentially ‘rogue’ applicants. However, my view, and that of the summit organising committee, is that it would act to discourage them if it is sufficiently detailed and stringent; it should deter practitioners who cannot meet those conditions. They will know in advance that they will not get support from other scientists, clinicians, regulators, local ethical review panels, journals, etc., unless the requirements have all been met. Once we have this kind of framework, countries can use it appropriately, adapting it into their own regulatory systems. But we do need to make sure that the rules and regulations we set now are flexible enough to account for rapid progress in the science and in the attitude of the public who may benefit.

Of course, this is not the first time that the development or application of a biological technique has shocked or concerned the public: recombinant DNA, the first IVF baby, Dolly the cloned sheep and mitochondrial replacement were all met with opposition when they were first announced. Is this case any different? I’m hoping that we get over the shock, and that genome editing of human embryos gradually becomes a viable and sensible approach to deal with some distressing genetic conditions.

When the first test tube babies were announced, the public and the media were generally very happy about it. But this was soon followed by a backlash. In that case, the backlash was driven largely by gut reactions and fear of dystopian futures coming from science fiction, although religious, ‘pro-life’ and anti-progress views also contributed. Of course, things then calmed down and IVF is now a well-accepted technique, albeit one where new developments still occupy the media. ‘Three-parent babies’ produced by mitochondrial replacement was also an approach that created a lot of fuss, but the notion behind it has become more widely accepted. Actually, I think this technique and its application represents a good lesson on how you should go about developing a new technology that applies to human embryos. Lots of hard work went into looking at the science, evaluating the clinical need, exploring the ethical issues, asking the public for their views, changing the law in the UK and establishing detailed regulations and guidelines, including considering the future welfare of the patients and any children born. Notably, all of this was carried out in an open manner, with all the preclinical scientific data published and active debate encouraged. Now, based on this process, other countries such as Australia and Singapore might change their regulations to make mitochondrial replacement possible. It’s a pity that JK did not follow this example.

 

This level of public exposure can only be good for the field and highlights the importance of establishing a dialogue with the public.

 

Overall, while JK’s behaviour has largely been deemed unconscionable by the scientific community, ethicists and others, I don’t think we should consider this a big setback to the field. JK seems to have been driven in part by ambition and a desire for fame – his motives were just wrong. But we should use his case as an opportunity to highlight how things should be done and how the vast majority of scientists – including developmental biologists – are actually very responsible. The whole affair has had another good outcome, in that it has certainly stimulated much wider debate than we ever thought would be possible. Just as a simple example, the organising committee of the first summit on Human Genome Editing in 2015 were delighted that between 6000 and 7000 people watched the live webcast. We had 1.8 million watch the live webcast this time. In addition, the worldwide media coverage means that many, many more people have been talking about the topic and thinking about these issues. Although some of this has stirred up negativity, this level of public exposure can only be good for the field and highlights the importance of establishing a dialogue with the public. Indeed, at the public event we ran in Hong Kong after the main summit finished, which was organised with the help of the Hong Kong Association for Rare Diseases and a local Café Scientifique, participants were critical of JK’s actions but were not negative about the potential uses of the technology. In fact, many realised that it could have great benefit. This just highlights that we need to talk more with the public about these kinds of techniques. Obviously, genome editing – in both the germline and somatic cells – needs to be considered. However, there are other techniques, such as culturing human embryos in vitro beyond the current 14-day limit, embryo-like entities and human-animal chimeras, that need to be debated. Another big issue is in vitro-derived gametes: if we can make eggs and sperm in vitro then this will change many things, not just in terms of research, but potentially in terms of reproductive options. All these ‘ethical minefields’ really need to be discussed more broadly, with a goal to develop flexible but robust regulation that can keep up with changes in both science and public attitudes.

I know that public engagement exercises are often expensive, and it is sometimes hard to reach out to people and give them the information that’s needed for them to be properly involved in these types of discussions. However, we clearly need participation from many more scientists and other relevant individuals (e.g. ethicists, regulators) to raise the level of the conversation with members of the public, not only to make sure that they are well informed, but also to seek their views. The decision of whether or not techniques such as genome editing in human embryos ever go into the clinic cannot be a decision made by scientists or clinicians alone; it has to be a decision that is made by all those concerned.

 

Acknowledgements

This article, which originated from an interview with Seema Grewal (Senior Editor, Development), is a personal reflection of the events that occurred prior to or at the Second International Summit on Human Genome Editing, and its style reflects this. I am indebted to my colleagues on the summit organising committee and from the Academies, and our hosts at the University of Hong Kong, who not only put together an excellent meeting but coped so well with the whole episode involving JK.

 

References

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Blakeley, P., Lea, R., Elder, K., Wamaitha, S. E., Kim, D. et al. (2017). Genome
editing reveals a role for OCT4 in human embryogenesis. Nature 55, 67-73.

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G. J., Wang, A. X. and Chen, H. S. (1993). Low frequency of the ccr5delta32 HIVresistance allele in mainland China: identification of the first case of ccr5delta32
mutation in the Chinese population. Scand. J. Infect. Dis. 31, 345-348. https://
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Ma, H., Marti-Gutierrez, N., Park, S. W., Wu, J., Lee, Y., Suzuki, K., Koski, A., Ji,
D., Hayama, T., Ahmed, R. et al. (2017). Correction of a pathogenic gene
mutation in human embryos. Nature 548, 413-419.

Ma, H., Marti-Gutierrez, N., Park, S. W., Wu, J., Hayama, T., Darby, H., Van
Dyken, C., Li, Y., Koski, A., Liang, D. et al. (2018). Reply. Nature 560, E10-E23.

Matos, A. R., Martins, J. S. C.C., Oliveira, M. L. A., Garcia, C. C., Siqueira, M. M.
(2019). Human CCR5Δ32 (rs333) polymorphism has no influence on severity and
mortality of influenza A(H1N1)pdm09 infection in Brazilian patients from the post
pandemic period. Infect. Genet. Evol. 67, 55-59.

Regalado, A. (2018). Chinese scientists are creating CRISPR babies MIT
Technology Review, 25 November. https://www.technologyreview.com/s/
612458/exclusive-chinese-scientists-are-creating-crispr-babies/.

Shioda, T., Nakayama, E. E., Tanaka, Y., Xin, X., Liu, H., Kawana-Tachikawa, A.,
Kato, A., Sakai, Y., Nagai, Y. and Iwamoto, A. (2001). Naturally occurring
deletional mutation in the C-terminal cytoplasmic tail of CCR5 affects surface
trafficking of CCR5. J. Virol. 75, 3462-3468. https://www.ncbi.nlm.nih.gov/
pubmed/11238872.

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(2018). Could failure in preimplantation genetic diagnosis justify editing the human
embryo genome? Cell Stem Cell 22, 481-482.

Zhou, M., Greenhill, S., Huang, S., Silva, T. K., Sano, Y., Wu, S., Cai, Y.,
Nagaoka, Y., Sehgal, M., Cai, D. J. et al. (2016). CCR5 is a suppressor for
cortical plasticity and hippocampal learning and memory. eLife e20985.

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Plant stem cells strive towards equality

Posted by , on 8 February 2019

By George Bassel and Iain Johnston

Multicellular organs consist of collections of cells which come together to achieve what individual cells cannot. The establishment of order in complex tissues has long been a subject of interest, dating back to the origins of microscopy itself.

Previous studies have proposed rules which predict when a cell will divide, using both its developmental age (adder) and size (sizer). Further studies in plants and animals have proposed rules which predict how a cell will divide by looking at the local geometry of a cell, it is predicted to occur using the shortest wall possible which passes through the centre.

These rules apply at the level of single cells, yet their consequences for multicellular tissues remain unknown. In other words, how these rules give rise to tissues, and the properties of these cellular arrangements, are not well understood.

Plants produce a striking diversity of structures, including the leaves and seeds that we eat. These above-ground parts of the plant all come from the stem cells in the so-called shoot apical meristem (SAM), a chaotic-looking mass of cells at growing tips of plants. These stem cells grow and divide to produce the structures that we see.

In Jackson et al., we investigated how the rules which govern the control of the cell cycle and placement of division plane act within the SAM to generate emergent properties in this collection of cells. Confocal laser microscopy and computer analysis revealed how the organization of cells in the SAM changes over time as cells divide. The microscope we used allowed us to reveal the internal structure of the SAM (see picture), and identify when and how cells divide. We then used network approaches, applied by neuroscientists to understand the organisation of brain cells, to reveal the global structure of cells in the SAM. In particular, we looked at “short paths” through the SAM – the routes that provide efficient ways of getting from cell A to cell B. We found an unexpected result: cell divisions occurred in a pattern that avoided short paths becoming overly reliant on individual cells. Once a cell begins to feature in many short paths across the SAM, it tends to divide in a way that provides a wider range of short routes connecting cells. This prevents individual cells from becoming too important in the movement of information, and creates a more equal community of cells.

 

Figure: Imaging the shoot apical meristem (SAM) over time allowed us to see which cells divided, and how they did so. We found that cells divided in such a way as to decrease the dependence of “short paths” through the tissue on individual cells.

 

As a metaphor, plant stem cells are organized more like a pre-planned North American City using a grid-like system, as opposed to the more heterogeneous street patterns seen in the Old World. This more homogeneous layout is more robust to failure – if any single path is compromised, it doesn’t cause a major traffic jam.

What might compromise a path through the SAM? It’s a part of the plant that, for example, is prone to herbivory (being eaten by pests). Ensuring that there’s a range of short paths through the SAM, rather than just one highway, means that if individual cells are eaten, information can still pass between cells.

Supporting this picture of robust information flow, we found that the homogenous organization structure appears to be important for the correct positioning of flowers. When the organisation is disrupted in mutant plants, flowers are misplaced. This supports the functional importance of this global equality of cells in the SAM.

This work provides a step forward in understanding how local cellular behaviour (when and how cells divide) gives rise to the global properties of tissues (robust short paths across the tissue). This is an example of “emergence”, where the actions of individuals give rise to surprising behaviour of the population as a whole. We hope that this quantitative picture will help advance our knowledge of how organs are designed and what functions they can fulfil.

 

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The people behind the papers – Masanori Kawaguchi, Kota Sugiyama and Yoshiyuki Seki

Posted by , on 8 February 2019

This interview, the 57th in our series, was recently published in Development


The molecular regulation of pluripotency has been most intensively studied in early mammalian development, but whether the transcriptional networks revealed in mouse and man also regulate pluripotency in other deuterostomes has remained unclear. A paper in this issue of Development now addresses the evolution of pluripotency with an analysis of the function of PRDM14 in zebrafish, amphioxus and sea urchin. We caught up with first authors Masanori Kawaguchi and Kota Sugiyama and their supervisor Yoshiyuki Seki, Associate Professor at Kwansei Gakuin University in Sanda, Japan, to find out more about the story.

 

Yoshiyuki (L), Kota (M) and Masanori (R)

 

Yoshiyuki, can you give us your scientific biography and the questions your lab is trying to answer?

YS From undergraduate to Master’s student, I trained as a cell biologist, supervised by Professor Hirofumi Kai at Kumamoto University. During this period, the Kai laboratory journal club started at 7:30 am every day, so I read a lot of papers, including a lot about developmental biology, and I decided to move to the developmental biology field for my PhD. As a PhD student, I began to investigate epigenetic reprogramming in primordial germ cells at Osaka University. I then did postdoctoral research at Mitinori Saitou’s laboratory at RIKEN, and identified that Prdm14 is specifically expressed in germline cells. Then in 2009, I got my independent position at Kwansei Gakuin University and, since then, have deeply analysed the function of PRDM14 in epigenetic reprogramming in pluripotent cells.

Considering the expression pattern and functions of Prmd14 in mice, the gene looks like the master regulator for germ cell specification. But even in humans, the expression pattern and functions are entirely different. A recent major aim of our lab is to uncover the origin and co-option of pluripotency networks during deuterostome evolution.

 

A recent major aim of our lab is to uncover the origin and co-option of pluripotency networks during deuterostome evolution

 

Masanori and Kota: how did you come to join the Seki lab, and what drives your research?

MK When I was an undergraduate, I was fascinated by the Seki lab’s research, and it was exciting to see Dr Seki performing experiments!

KS When I was an undergraduate student, I was interested in research about pluripotent stem cells and also fascinated by the evolutionary history of pluripotency networks, both questions that the Seki lab works on. My driving force for research is curiosity to uncover unknown mechanisms.

 

What was known about the evolutionary history of the mammalian pluripotency network before your study?

MK, KS & YS The mammalian pluripotency network has been deeply analysed using mouse embryonic stem cells. This network is regulated by the core transcriptional regulatory circuitry that is centred on POU5F1 (OCT4) and NANOG. However, the pluripotency network in non-mammalian deuterostomes has remained largely unknown. Recent studies of the genomes of several deuterostome species have suggested that Pou5f1 and Nanog might appear on the genome at around the emergence of cartilaginous fishes. Because Pou5f1 and Nanog are expressed in pluripotent cells in the axolotl embryo, these factors have already been integrated into the pluripotency network at around the emergence of urodeles during vertebrate evolution.

 

Can you give us the key results of the paper in a paragraph?

MK, KS & YS Our paper shows that Prdm14 is specifically expressed in motor neurons of the amphioxus embryo, similar to the pattern that is observed in the zebrafish embryo. Before getting this result, we thought that the expression pattern of Prdm14 in the zebrafish embryo might be a specific phenomenon, because the synteny of Prdm14 is specifically not conserved in the zebrafish genome. Conservation of Prdm14 expression in motor neurons among non-tetrapod vertebrates led us to a novel concept: the co-option of PRDM14 from motor neurons into pluripotent cells might be crucial for the stabilization of the undifferentiated state in pluripotent cells in the early embryo of amniotes.

 

Why do you think amniotes needed a new transcriptional circuitry to regulate pluripotency?

MK, KS & YS A major difference in early embryogenesis between non-amniotes and amniotes is the complexity of the extra-embryonic tissues. In amniotes, the undifferentiated state of pluripotent cells needs to be maintained before the maturation of extra-embryonic tissues, especially in mammals. We speculate that the stabilization of the pluripotency network – by integrating the PRDM14-CBFA2T complex in pluripotent cells – might provide the evolutionary competence for creating de novo extra-embryonic tissues during amniote evolution.

 

Prdm14 expression in amphioxus motor neurons.

 

What do your experiments using sea urchin PRDM14-CBFA2T suggest about the deeper evolutionary function of the complex?

MK, KS & YS The function of the PRDM14-CBFA2T axis has not yet been analysed in the early embryo of echinoderms such as sea urchins. Previous studies have shown that sea star PRDM14 is expressed in the embryonic gut, a multipotent tissue that has the capacity to create primordial germ cells. Our compensation assay using sea urchin PRDM14 and CBFA2T completely rescues the defect of self-renewal in mouse embryonic stem cells lacking mouse PRDM14 and CBFA2T2. This suggests that the PRDM14-CBFA2T complex might be involved in the maintenance of multipotency in the sea star.

 

When doing the research, did you have any particular result or eureka moment that has stuck with you?

MK My most exciting moment was when I performed immunoprecipitation to elucidate the relationship between the PRDM14-CBFA2T interaction and the maintenance of self-renewal of mouse Prdm14 knockout (KO) embryonic stem cells.

 

KS I was really excited when the combined expression of sea urchin PRDM14 and CBFA2T rescued the self-renewal defect in mouse Prdm14 KO embryonic stem cells. We expected that the binding capacity of PRDM14 orthologues with CBFA2T would have been acquired during the evolutionary route to chordates after the splitting from the common ancestor with echinoderms.

And what about the flipside: any moments of frustration or despair?

KS I used several cell lines to detect the interaction of PRDM14 orthologues and mouse CBFA2T2 using immunoprecipitation. To obtain the clear band in all conditions, I had to perform immunoprecipitation-western blotting repeatedly, which was quite frustrating!

 

So what next for you two after this paper?

MK Since finishing my Master’s course in 2017, I have been working at a food company as a researcher.

KS I recently identified new molecules regulating the transition from pluripotent stem cells into the so-called two cell-like cells. In the future I would like to investigate the evolutionary conservation and diversity of the zygotic genome activation pathway, using mouse and newt.

 

Where will this work take the Seki lab?

YS Comparing the expression pattern and function of PRDM14 offers a framework for addressing how pluripotency transcriptional networks evolve in deuterostomes. We are interested in when and how PRDM14 integrated into pluripotency networks from motor neurons. We consider urodeles and reptiles to be key organisms for determining the integration timing of the PRDM14-CBFA2T complex in pluripotent cells. We are also trying to identify the cis-regulatory elements that are required for PRDM14 expression in pluripotent cells in mice and human. Interestingly, the expression pattern of PRDM14 is quite different between mice and human, and the mouse epiblast displays a unique epiblast morphology (referred to as an egg cylinder) whereas the human epiblast forms a disc. We expect that the identification of a rodent-specific cis-regulatory region of PRDM14 might contribute to our understanding of morphological differences in the epiblast of rodent and non-rodent mammals.

 

Finally, let’s move outside the lab – what do you like to do in your spare time in Sanda?

YS Sanda city has a lot of beautiful nature and parks. When my two children were pre-school, I often took them to these parks and also went hiking with my wife. Recently we’ve been taking my son to football and basketball club, and we play together every weekend.

 

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Scientific Coordinator in Epigenetics at Helmholtz Zentrum München (HMGU)

Posted by , on 7 February 2019

Closing Date: 15 March 2021

 

Epigenetics research is central to understanding environment-genome interactions, which in turn is fundamental to advancing environmental health research, the key focus area of Helmholtz Zentrum München (HMGU). The strength and unique nature of epigenetics research conducted at HMGU is its broad range of research areas such as cellular plasticity and stem cell research, diabetes research, computational biology, metabolism, modeling of single cell fate decisions, systems biology, development, immunology and epidemiology, as well as the combination of basic and translational research approaches. The Management and Strategy Office for Epigenetics & Stem Cell Research develops and coordinates new initiatives and programs to position the broad field of epigenetics internationally.

We are looking for a Scientific Coordinator in Epigenetics who will be part of an international team shaping the epigenetics field beyond Munich. He/she will ensure the overall coordination of activities of the epigenetics@hmgu community and provide scientific support for the founding institutes: Institute of Epigenetics and Stem Cells (IES) as well as Institute of Functional Epigenetics (IFE).

Specific responsibilities are

• Coordination of the Internship Programme in Epigenetics, Cellular Plasticity and Stem Cells.
• Supporting the founding institutes regarding fellowship applications and grants
• Regular reporting on activities
• Social Media and website management:
• Event management: Organisation of seminars, community meetings and conferences
• Outreach activities: Establishing new international networks and partnerships
• Regular participation in lab meetings as the community representative
Your qualifications
• PhD degree in the Life Sciences, with a broad knowledge of fundamental biology and a particular interest in epigenetics
• International work experience in a scientific environment
• Experience in scientific project management
• Knowledge of concepts and instruments for the promotion of young scientists is highly desirable
• Excellent organizational and communication skills
• Proactive engagement in a team-oriented work environment
• Friendly and approachable, with excellent communication and personal skills
• Fluency in English is essential

• Knowledge of content management systems (Typo3) desirable

 

Link to the application:

https://bms.candibase.de/atool/helmholtz/frontend.php?view=04c5b0957f9eeb1a9263a485864ca3db&lang=en&

 

For more information contact Dr. Astrid Lunkes

 

 

 

 

 

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Funded places for early-career researchers at a Company of Biologists Workshop in July

Posted by , on 7 February 2019

This summer, the Company of Biologists, the not-for-profit publisher of Development, is running a Workshop on ‘New frontiers in the brain: unexpected roles of the choroid plexus-cerebrospinal fluid system in health and disease‘, organised by Fiona Doetsch and Maria K. Lehtinen. It will cover various bases, many of which intersect with developmental biology:

1. Choroid plexus/CSF signaling niche: development, stem cells and plasticity
2. Barrier and neuroimmune function
3. Propelling and sensing the CSF: ependyma and cilia
4. Novel signaling sources: extra-axial CSF, Interstitial fluid, meninges
5. Choroid plexus/CSF and disease

The Company of Biologists Workshops provide leading experts and early career scientists from a diverse range of scientific backgrounds with a stimulating environment for the cross-fertilisation of interdisciplinary ideas. The programmes are carefully developed and are intended to champion the novel techniques and innovations that will underpin important scientific advances.

There are currently multiple funded spaces for early-career researchers to attend this exciting event (deadline = 15 March). To find out more and apply online please visit

biologists.com/workshops/july2019

 

 

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Hox genes: the key to decipher limb position – the story behind the paper

Posted by , on 6 February 2019

In our recent paper published in Current Biology, we unravel the direct and early role for Hox genes in the regulation and natural variation of the forelimb position in birds. Here I will share with you the story behind this paper.

I have always been fascinated by the question of how, from a single cell, a multicellular organism with a complex, highly organized three-dimensional structure can arise. Therefore, when I started my PhD in Dr. J. Gros’ lab and got the opportunity to work on the question of limb position in chicken embryos, I was thrilled. How limbs reproducibly form along the vertebrate body is a fascinating, long standing question for developmental but also for evolutionary biologists. Indeed, this question has two main aspects:

  1. one purely developmental aspect – in trying to understand the cellular and molecular mechanisms establishing limb position during the embryo development
  2. one evolutionary aspect – in tackling the question of diversity in limb position amongst tetrapod species.

 

The context

In tetrapods, while limbs always position at the level of the cervico-thoracic (for the forelimb) or lumbo-sacral (for the hindlimb) vertebral transitions, the position of these vertebral frontiers – and hence the limb position – is highly variable between species. Avian species especially, display a wide variation in the position of their forelimb – from the sparrow that form forelimbs at the level of the 10th vertebra up to the swan in which forelimbs form at the level of the 25th vertebra – a difference of no less than 15 vertebrae!

Despite major advances in our understanding of limb patterning in three dimensions, how limbs reproducibly form along the anteroposterior axis and how variations in these positions arise remained largely unresolved. Hox genes were long suspected to regulate limb position (Tanaka, 2013; Tickle, 2015). This assumption first arose because of their well-demonstrated role in patterning the vertebrae and was further supported by cross-species comparative studies which showed that Hox gene expression domains correlate with limb position in different species (Burke et al., 1995). But the different supportive evidences were mostly correlative (Burke et al., 1995; Cohn et al., 1997; Minguillon et al., 2012; Nishimoto et al., 2014). In addition, whereas Hox gene mutant mice display vertebral identity transformations (Mallo et al., 2010), functional studies in support for a role of Hox genes in regulating limb position were lacking. Therefore, whether Hox genes would control limb initiation and position was clearly unresolved at the time we started this work.

 

Our Results

Where do the limbs come from? They originate from the Lateral Plate Mesoderm (LPM), a mesodermal tissue that flanks axial embryonic structures (i.e. notochord, neural tube and somites), and will emerge from this tissue at their stereotypical position, at three days of development (Hamburger and Hamilton stage 15). First, we wanted to determine when the forelimb position is primarily established. We took advantage of the possibility to do grafting experiments in chicken and quail embryos, combined with the use of transgenic quail lines generated in the lab, to establish that the forelimb position is determined very early, 24h before limb initiation (i.e. at stage 11, 2 days of development).

The finding that the forelimb position is already established by stage 11 led us to think that this positional information could be established earlier – during the process of gastrulation. Gastrulation is this key morphological process during which the three germ layers – ectoderm, mesoderm and endoderm – are formed. The LPM is generated during this process and we wondered whether it was also patterned into limb- and non-limb domains while being generated. Whereas LPM precursor cells in the epiblast had been identified through lineage-tracing experiments (Psychoyos and Stern, 1996), how the forelimb, interlimb and hindlimb cells are generated was not characterized. The process of gastrulation is really dynamic and spans for about 24h. Therefore, in order to precisely catch the dynamic behaviors of LPM precursor cells, we used yet again another advantage of the chicken embryo, which is the possibility to do live-imaging, especially in the early stages of development as the embryo is flat and can be cultured ex ovo. We therefore performed a dynamic lineage analysis of the LPM formation, and could nicely characterize that the forelimb, interlimb and hindlimb domains are sequentially generated during gastrulation.

At this point, we had described how the LPM is formed and patterned into limb and non-limb domains at the cellular level. The next step was now to investigate the molecular mechanism underlying this process.

As I mentioned earlier, our top candidates for the regulation of limb position were the Hox genes, well-known for their role in patterning vertebrae along the main body axis (Mallo et al., 2010). For our study, it is important to remember that these genes are arranged in four different clusters and display a specific chromosomal organization that reflects their sequence of activation (i.e. temporal collinearity) and their successive domains of expression along the antero-posterior axis (i.e. spatial collinearity) (Izpisúa-Belmonte et al., 1991). Interestingly, we noticed that the collinear sequence of Hoxb genes activation during gastrulation correlates with the temporal sequence of forelimb (e.g. Hoxb4) and interlimb (e.g. Hoxb7and Hoxb9) formation we had just identified, suggesting that they could play a role in the formation of these domains. To test it, we used the electroporation technique that allowed us to do functional perturbations precisely controlled in time and space. We performed overexpression and loss-of-function of different Hoxb genes in LPM precursor cells to perturb their activation during gastrulation. We could show that – as previously identified in the paraxial mesoderm (Iimura and Pourquié, 2006) – Hox genes, collinearly activated during gastrulation, establish their own stereotypical sequential expression domains in the LPM – domains that correlate with the forelimb (e.g. Hoxb4) and interlimb fields (e.g. Hoxb7 and Hoxb9).

 

But are these Hox expression domains important to position the forelimb?

One year before I started my PhD, a study showed that Hox4/5 genes could bind to a regulatory sequence of Tbx5 – a transcription factor essential for forelimb initiation – and activate the expression of a reporter gene under the control of this regulatory sequence (Minguillon et al., 2012). These results further supported a role for Hox genes in positioning the forelimb along the antero-posterior axis. We therefore decided to ectopically express Hoxb4 in the interlimb at stage 14 – when Hox domains are well-established – to see if we could perturb the forelimb position. We first screened embryos for an ectopic expression of Tbx5 in the interlimb, naively thinking that Hoxb4 overexpression should first induce Tbx5 expression. But that would have been too simple, Hoxb4 alone was not able to induce Tbx5 ectopic expression in the interlimb…

We were initially quite puzzled by this result. But the story could not stop there, we were missing something and we had to find out what. Then became a long journey during which we electroporated many different combinations of genes in the interlimb – e.g. Hoxb4 fused to VP16; combined Hox4/Hox5 genes; Hoxb4 plus activators of Retinoic Acid or Wnt/β catenin pathways, both involved in Tbx5 expression and forelimb initiation (Nishimoto et al., 2015); and several others – in an attempt to induce Tbx5 expression in the interlimb and a shift in limb position. Unfortunately, none of these combinations had an effect on Tbx5 expression nor limb position. At this point, we started to be somewhat desperate and were about to give up as the end of my PhD was getting closer. But reading again some of the literature, we came back to one paper in which it was shown that Hoxc9 – which is expressed in the interlimb – could repress Tbx5 expression (Nishimoto et al., 2014). Maybe the solution was there, this repressive activity was preventing all our attempts to posteriorly extend the Tbx5-positive forelimb field. This was it, the last-chance experiment! We decided to construct a dominant-negative form of Hoxc9 using a strategy others had established to generate Hox dominant-negative constructs (Denans et al., 2015). Then, we combined overexpression of Hoxb4 together with the repression of Hoxc9 in the interlimb and, not only we could nicely extend the Tbx5-positive forelimb domain in the interlimb, but we could displace the final forelimb position (Figure 1). There it was, many years after Hox genes where first suspected, we finally had the functional evidence of their direct role in regulating the forelimb position!

 

Figure 1: Electroporation of Hoxb4+Hoxc9dn in the right interlimb domain of stage 14 chicken embryos induces a posterior extension of the Tbx5-positive forelimb field (st14+24h), a posteriorly extended forelimb bud (st14+48h) and ultimately posteriorly shifted forelimb (st14+4 days – Alcian Blue staining)

 

Importantly, removing Hoxc9 repression from the interlimb alone was not sufficient to induce Tbx5 expression and limb initiation. Therefore, showing that to change the forelimb position, both a shift of the forelimb field (e.g. Hoxb4 expression) and the interlimb field (e.g. Hox9 expression) is necessary. These results brought to us one potential explanation to why the vast majority of Hox genes mutant mice do not show major perturbations in limb position. Indeed, our data argue that, to induce a shift in the forelimb position in mouse, a combination of gain-of-function for forelimb activator (e.g. Hoxb4) and loss-of-function for forelimb-repressor (e.g. Hox9) should be performed. Another interesting point worth commenting is that, while Hoxb4 and Hox9 activate and repress Tbx5 expression, eventually leading to the establishment of the definitive forelimb position, Tbx5 itself was shown to be not sufficient to induce limb initiation (Nishimoto et al., 2015). Therefore, implying that, to regulate forelimb initiation at its specific position, Hox genes do not solely act upon activation/repression of Tbx5. This point remains to be explored but one can speculate that Hox genes could activate/repress other regulators of limb initiation or act cooperatively with Tbx5 to activate the limb initiation program, as recently shown for Hoxc10 and Tbx4 in the context of hindlimb development (Jain et al., 2018).

 

At this point, we had now unraveled the developmental mechanism behind limb position establishment. But what about limb position diversity, how can variations in limb position arise?

Our results suggested that natural variations in the forelimb position should be traced back to changes in Hox genes activation during gastrulation. To test this hypothesis, we took advantage of the bird natural variation in limb position. We selected three different bird species: zebra finch, chicken and ostrich as they form forelimbs at the level of the 13th, 15th and 18th vertebra, respectively, to perform a cross-species comparative analysis of Hoxb genes temporal and spatial dynamics of expression during early development. We then could provide evidence that, as predicted, changes in the timing of Hox activation during gastrulation prefigure variation in the spatial organization of these genes – i.e. in the spatial position of Hoxb4/Hoxb9 border of expression – in the LPM and ultimately, natural variation in forelimb position in birds. Working with non-conventional model organisms such as the ostrich was not trivial and required some troubleshooting and optimization at every step of the process, but it brought us with some very exciting outcomes and I think, shows the importance of using non-traditional model organisms when it comes to challenge and validate the models and predictions we establish using our favorite model organisms.

Finally, now that we had established the role of Hox genes in regulating limb position and variation, the next logical step was to investigate how such variation in Hox activation timing could be controlled. We got interested in the Retinoic Acid (RA) signaling pathway, and especially the RA catabolizing enzyme Cyp26a1, as it was already shown to be involved in hindlimb position regulation (Lee et al., 2010). We observed that Cyp26a1 onset of expression differs between the three avian species – i.e. its expression is premature and delayed in zebra finch and ostrich embryos, respectively, compared to chicken – consistent with a role for RA signaling in regulating Hox genes activation. Finally, modulating RA signaling during gastrulation in chicken embryos, provoked changes in Hox genes spatial organization in the LPM and in the Tbx5-positive forelimb field position, further suggesting that RA signaling might regulate the forelimb position through the regulation of Hox genes activation during gastrulation. This is an interesting point that will definitely need to be further investigated. Indeed, the possibility that Cyp26a1, already shown to regulate hindlimb position (Lee et al., 2010) could also regulate the forelimb position is particularly interesting. Especially, as it was recently proposed that differences in the onset of Gdf11 expression – i.e. the signaling molecule that induces Cyp26a1 expression – account for variations in hindlimb position amongst tetrapods (Matsubara et al., 2017). Therefore, one single signaling pathway would then be responsible for the regulation and natural variation of both fore- and hindlimb position.

 

Conclusion

From all these different results, the major conclusion of our work is that the forelimb position is determined very early, during gastrulation: it is the temporally controlled activation of Hox genes that progressively patterns the LPM into limb- and non-limb forming domains, as the main axis is being formed. And relative changes in this timed collinear activation underlie natural variation in forelimb position in birds (Figure 2).

One of the important points brought by our study is that we show the LPM is patterned by Hox genes during gastrulation following a similar mechanism as the one identified to pattern the somites (Iimura and Pourquié, 2006). These two tissues – that respectively give rise to the limb and vertebrae – both being generated and patterned during gastrulation by Hox genes, offers a simple mechanism to pattern the cervico-thoracic frontier in the somites and the forelimb position in the LPM, concomitantly therefore maintaining their tight association observed in all tetrapod species.

 

 

Figure 2: Hox genes, collinearly activated during gastrulation, establish their collinear spatial expression domains in the LPM and, within these domains, Hoxb4 anteriorly and Hox9 posteriorly, respectively activate and repress limb initiation (i.e. Tbx5 expression) therefore defining the definitive limb position. Relative changes in the temporal sequence of Hox activation underly natural variations in limb position in birds.

 

 

As a conclusion, our work that combines experimental embryology, state-of-the-art live imaging and cross-species comparative studies, addresses the major question of how the forelimb position is determined and solves a 20-year long controversy on the role of Hox genes in regulating limb position. It also provides a general mechanism for generating variation in body plan organization in vertebrates and reinforces the importance of Hox genes in shaping animal body plans.

 

 

Chloé Moreau

 

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