Epithelial tubes perform crucial functions in various organs, providing routes for the transport of fluids and gases. A new paper in Development addresses the question of how epithelial tubes elongate during development, using a combination of mouse organ culture and mathematical modelling. To find out more about the work, we met four of its authors: PhD students Lisa Conrad and Steven Runser, senior scientist Roman Vetter, and their supervisor Dagmar Iber, Professor in the Department of Biosystems Science and Engineering at ETH Zurich.
Lisa (top left), Steve (top right), Roman (bottom left) and Dagmar (bottom right).
Dagmar, can you give us your scientific biography and the questions your lab is trying to answer?
DI: I studied mathematics and biology, and did Masters degrees and PhDs in Cambridge and Oxford in each field. Since the very start, I have been interested in using mathematical modelling to uncover biological mechanisms. A Junior Research Fellowship at St. John’s College in Oxford gave me the freedom to pursue my own ideas and develop more precise, data-based models than the established conceptual models. Initially, I worked in immunology, but then switched to cell differentiation in bacteria, as the required quantitative data to build and validate models was available only for such simple organisms. These days, my group focuses on developmental mechanisms all the way up to human, and although we mostly collaborate with experimental groups, ETH allows me to also run a small wet lab to generate data and test ideas. The lab largely focuses on mouse lung and kidney development, but we maintain a rather broad interest in fundamental patterning mechanisms, and also collaborate with clinicians.
Roman, can you tell us a little about your research history and how you ended up working on developmental questions?
RV: I’m a computational physicist by training, and did my studies and PhD at ETH Zurich. With a few exceptions, my interest has always been in explaining nature’s wealth of emergent complex behaviour from simple, fundamental principles. During the earlier stages of my academic career, I found these problems mainly in the physical disciplines – from snow metamorphism to filament packing to crumpled shells and even fuel cell simulations. If you go through life with an open mind, open eyes and open ears, there’s an interesting question calling for a quantitative explanation virtually everywhere. My attention is drawn easiest by questions that combine geometrical shapes with mechanics and patterning. Lately, I have found such inspiration more and more in biology, where fundamental aspects of morphogenesis and development require taking new vantage points to advance further. I joined Dagmar’s group 2 years ago when she was looking for a senior biophysics modeller and I was looking to enter the field of computational biology to find new puzzles to solve – it was an instant match. I started as a postdoctoral researcher and recently became a senior scientist and lecturer in her group.
Lisa and Steve – how did you come to work in Dagmar’s lab and what drives your research today?
LC: I studied biology at the University of Freiburg and molecular medicine at Uppsala University. Developmental biology has fascinated me from the beginning; besides the interesting questions and methods in this field, the beauty of development is just so captivating! During a variety of lab projects, I noticed how much I enjoy projects that bring together expertise from different scientific backgrounds. By applying to the Life Science Zurich Graduate School, I found out about Dagmar’s group and got curious about their multidisciplinary approach to developmental biology. I started as the first PhD student with an experimental focus in the group’s then recently opened wet lab, eager to build on my experimental and research skills, while learning about new ways on how to tackle developmental questions from a different angle. It has been challenging to keep up with the aspects of the group’s research that are far from what I studied, but it’s also immensely rewarding when we can join forces to find new ways to better understand organ morphogenesis!
SR: I started my studies in cellular and molecular biology at the University of Strasbourg, but I quickly deviated towards more computational fields. I have always been interested in the design and application of mechanical simulations for the study of biological systems. To respond to this interest and to learn more about numerical approaches, I applied to Dagmar’s lab to do my master’s thesis. After completion of the thesis a little less than 2 years ago, Dagmar offered me the opportunity to continue in this field as a doctoral student. Since then, I have been developing and using different types of simulation models to study organ growth and morphogenesis.
How did you come to study tube elongation?
DI: The group had long been interested in lung and kidney branching morphogenesis. Although our ligand-receptor-based Turing mechanism could nicely predict where new branch points would form during lung and kidney branching morphogenesis, we noticed that the branch shapes that emerged in our simulations looked nothing like in the embryo because we were missing that bias in outgrowth that lets epithelial tubes of embryonic lungs and kidneys lengthen more than they widen.
Before this project, what mechanisms had been proposed for biased tube elongation?
DI: In lungs and kidneys, chemotactic movement towards a source of FGF10 or GDNF had long been noticed, and the extracellular matrix is thinner at the bud tips. In mammary glands, a constricting force had been proposed. In plants, hoop stress is a popular theory to explain their biased growth. We tested all those ideas, but none could explain the biased outgrowth of embryonic lung or kidney tubules. In fact, when checking the potential of hoop stress, we noticed that the lumen of the tubes is mostly very narrow, whereas the wall, the epithelium, is comparably thick. Although this is inconsistent with a role of hoop stress, it gave us the idea that fluid flow-induced shear stress may play a role.
Fluid flow (arrows) from tip to base in the lumen (green) of developing lungs causes shear stress levels strong enough to be sensed by epithelial cells (magenta), giving them a direction in which to preferentially grow. This discovery provides a new explanation for the stereotypical directional bias in tube outgrowth observed during the development of branched organs such as lungs and kidneys.
Can you give us the key results of the paper in a paragraph?
SR: The key result of the paper is that the observed bias in epithelial tube outgrowth, the accompanying bias in the apical cell shape and the resulting biased orientation of cell divisions, can be explained with fluid-flow driven shear stress. After having ruled out all the previously proposed mechanisms, Roman used a Finite Element method to demonstrate that the collapse of the tubes in itself was very unlikely to result in a bias in outgrowth. Instead, the narrow luminal region meant that a fluid flow in the epithelial tubes might cause a significant level of shear stress on the cell walls. To prove the existence of a flow, Lisa injected micro-beads in the lung lumens and observed their movements over time. We simulated the effect that a flow with the measured velocity would have on the cell walls of a similar lung tube geometry. The shear stress levels thus calculated were well within the range of what epithelial cells can sense. Shear stress is well known to result in the elongation of endothelial cells along the flow direction in blood vessels. I used a cell-based vertex model to investigate the impact of such an elongation on epithelial tissues. Once parameterized based on quantitative data, the model was able to recapitulate all the measured features of the lung and kidney tube epithelium. The bias in cell division orientations was well in line with what had been measured, and similarly the bias in outgrowth of the tissue matched with the experimental observations.
How do you think lung and kidney cells sense shear stress, and how is this sensing translated into biased growth at the tissue level?
DI: Epithelial cells can sense shear stress with their cilium. How they translate this into a change in cell shape, and how the extent of the cell shape change relates to the shear stress level is not known. Microfluidic experiments may help to resolve this.
Do you have any ideas for what causes tube collapse in early development?
RV: Indeed we do have some ideas, and we’re working toward testing possible theoretical explanations with detailed computer simulations by Steve, and toward validating them with experimental data from our wet lab, together with Lisa and other group members. Tube shape and collapse is an exciting topic of ongoing research in our group, and we’re looking forward to telling you more once we have conclusive answers.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
LC, SR: The project really picked up momentum when Harold Gómez, who is also shared first author, noticed, through careful examination of his beautiful lightsheet microscopy data, that the lumen is very narrow in many parts of the lung. But the most exciting moment was when we simulated the shear stress produced by the fluid flow, which we had finally succeeded in measuring experimentally, and realized that it was within the range cells can sense.
The most exciting moment was when we simulated the shear stress produced by the fluid flow.
And what about the flipside: any moments of frustration or despair?
DI: For me, certainly the first response by the referees. For years, I had asked experimental colleagues how to measure fluid flow in lung or kidney tubules and discussed strategies with my team. Yet, no one in my group felt they could pull this off. So, I decided to send the paper to Development, hoping that it would inspire some experimental lab to do that last experiment. After all, through a combination of (simple) experiments and simulations (that encompassed many different sophisticated techniques) we had excluded all previous proposals, suggested a new one, and provided convincing evidence for it. Yet, the referees would not have it. They not only insisted on that last experiment, but also saw little value in the paper as it was. I have seen it more than once that junior members got driven away from science by referee reports that had failed to recognise the value of their work. But not so Lisa: realising that those fluid-flow measurements were the make-or-break, she decided to just give it a try – despite all COVID restrictions. She remembered that Renato Paro had left an injector to our department when retiring, which no one used. She got it to work with the help of his former technician – and demonstrated fluid flow at the required level in the developing lungs.
LC: For me, the biggest source of frustration is when an experiment fails due to technical issues and the tissue samples that I harvested from an animal go to waste. Regarding the referee reports, Dagmar encouraged us to take on the challenge, and celebrating the small successes along the way kept spirits up! In the end, confirming our proposed mechanism was a really good experience.
How has your research been affected by the COVID-19 pandemic?
LC: Last year in March, ETH went into lockdown to help slow down the spread of the virus and our lab was closed for about 6 weeks. The reopening was done in several phases, so we had to work in shifts for a while and it took some time to start up experiments again. Working in shared facilities is still restricted, but most of the time we can figure that out by communicating with colleagues and working around each other’s schedules. In general, everything needs a bit more planning now. For the paper revisions, we had to set up a new experiment in the lab while COVID-19 restrictions were still in place, which of course provided an extra challenge. Having a colleague take a look at your (failed) experiment usually speeds up optimization and trouble-shooting and there are fewer opportunities for spontaneous exchange with other groups. Despite the additional work and stress brought by the pandemic, I feel like everyone at BSSE is supporting each other; especially Makiko Seimiya and Tom Lummen (BSSE Single Cell Facility), who have been awesome in sharing their advice and equipment, and helping me with many tries at the spinning disk confocal, which was a new microscopy system for me.
DI, RV, SR: As theoreticians, we have been forced into a home office for more than a year now. We miss the personal interactions, but remote work is otherwise straightforward for us.
What next for you two after this paper?
LC: I am currently finishing up a project that compares branching morphogenesis in lungs and kidneys. In a collaboration with Roman and other team members, we’re also looking at tube formation, where I’m using nephrogenesis in kidney organoids as a model.
SR: The 2D vertex model used in this paper offers many possibilities for the study of tightly packed cell sheets. However, numerous developmental events can only correctly be represented in three dimensions. With the advent of high performance computing, new computational frameworks representing cells more realistically in 3D can now be developed. I am currently developing such a model specifically designed for the simulation of epithelial tissues.
Where will this story take the Iber lab?
DI: The mechanism that defines the aspect ratio of tubes is one important puzzle piece to explain how complex organs are shaped and how organ-specific differences arise. There are many other fundamental questions concerning tubulogenesis, epithelial organisation, the physics of budding, the role of the mesenchyme and the final reorganisation of the lung epithelial tree into a fractal-like architecture. As a group, we are interested more generally in self-organisation during development.
Finally, let’s move outside the lab – what do you like to do in your spare time in Basel?
LC: I picked up diving a few years back and it’s so much fun! For a local spot, I would recommend the Bodensee; it’s really amazing to dive into a whole new world ‘at home’, now that travelling hasn’t really been an option. Basel has lots of relaxing greenery and I often go for walks along the Rhine. Since the start of the pandemic, I have also rediscovered the fun in crafting and caring for plants on my balcony.
SR: I enjoy a lot of different activities, which range from reading historical novels to playing football.
RV: Spare time comes and goes in phases. There are more things I’d enjoy doing than I could possibly fit into a full day – cycling across the country is one of many.
DI: I enjoy the Swiss mountains, swimming in the Rhine, the tennis court in front of my house – and the preparation for SoLa, the yearly running relay race, which we participate in with the entire group.
Hello all! I am Viktoria, the Sustainable Conferencing Officer of The Company of Biologists. I am here to quickly answer some questions about our Sustainable Conferencing Initiative.
What is the aim of the Initiative?
As biologists become increasingly aware of their environmental and social impact, questions about the environmental sustainability and social responsibility of our events have become more prominent. The Company of Biologists launched the Sustainable Conferencing Initiative in October 2020 to provide guidance and support on the sustainability of events. Furthermore, acknowledging the changes that the pandemic has brought on virtual communications, we are also here to offer insights into technologies that can be used for virtual and hybrid events. Our main aim is to facilitate the discussion of sustainability issues and innovative technologies in our community.
How will you share information?
We have our own website! You can visit sustainability.biologists and browse through our different pages. There is a Blog page where our team publishes pieces of information based on the questions coming from our community, and a Resources page that lists useful links regarding sustainability and innovative technologies. Also, in June our Forum became live. Its purpose is to offer a space to our community where ideas, best practices and questions can be shared, and we can all learn from and help each other.
Is there another form of support available?
Sustainable Conferencing Grants are available to fund innovative ideas that enable biologists to collaborate productively while minimising their impact on the environment. We accept applications from organisers of meetings, workshops, conferences, seminars, training events, and a wide range of activities in the fields covered by our journals. The events can be in-person, virtual or hybrid. Moreover, applicants for Scientific Meeting Grants may be awarded an additional £1,000 if they can demonstrate efforts have been made to reduce the environmental footprint of their event.
How can anyone join the discussion?
Visit our site to explore the information we share. If you register for an account, you will automatically gain access to our Forum where you can ask questions, offer advice, and engage with the community on sustainability and new technologies issues. You can also join our mailing list to receive our newsletters (we promise no spam emails).
Furthermore, you can find us on Twitter as @COB_Sustainable Come join us there and share ideas or questions by using our hashtag #Sustainable_Conferencing. Of course, you can always contact us via email at sustainability@biologists.com.
We are looking forward to connecting with our community and starting the discussion!
Over on The Company of Biologists WeChat channel, we’re enjoying getting to know the growing community. We recently published an interview with Dr Zhiyi Lv, a member of Professor Bo Dong’s group at Ocean University China in Qingdao, China. The Dong lab was established in 2014 and is interested in uncovering the cellular, mechanical and biochemical signalling networks that interact to drive the diverse morphogenetic processes during organ formation and tissue regression using marine ascidians and flies as models. You can find out more about Bo’s research in a ‘The people behind the papers’ interview published in Development last year and a recent Development presents… talk by Hongzhe Peng, a doctoral student in the lab.
Having gained his undergraduate and Master degrees at Northwestern A&F University in China, Dr Lv moved to Germany to obtain his PhD at the University of Göttingen. He remained there for his first postdoc position before relocating back to China to join Professor Bo Dong’s lab at Ocean University of China. Here, he tells us more about his scientific journey, including why he finds the dev bio field amazing and how labs differ between Europe and China.
When did you first become interested in science?
I don’t think there was a specific timepoint that where I thought, ‘aha, now I am interested in science!’ All kids are curious about the unknown world and they are always trying to explore the surroundings. In this way, scientists and children have a lot in common. Fortunately, I did not lose this curiosity as I grew up.
What attracted you to the field of developmental biology?
How a simple-structured (relatively) fertilised egg becomes a complex adult with head and legs attracted so many people since Aristotle’s time. Then, people realised that genes controlled the development. Now, increasing evidence suggests that mechanical forces contribute morphogenesis actively. It is amazing, isn’t it?
You gained your PhD at the University of Göttingen in Germany and stayed in the same lab for your postdoc but switched from biochemistry to biophysics of morphogenesis – can you tell us more?
I got my PhD under the supervision of Professor Grosshans. I worked on the regulatory mechanism of actin polymerisation. At that time, we identified that a F-BAR protein, Cip4, inhibits actin polymerisation by inactivating Diaphanous, which is an actin nucleator. We got very exciting data, which was published in Journal of Cell Science. Biophysics of embryogenesis has been an important topic in the Grosshans lab. I was impressed by my biophysical colleagues’ talks during our seminars. Professor Grosshans was very nice and always encouraged us to explore a new area. Two projects were running in the lab. One was mechano-transduction at cell-cell contact, and the other one was nuclear array self-organisation in a Drosophila syncytial embryo. I chose the second one for my postdoctoral project.
What are the differences in the lab between Europe and China?
The biggest difference is that experienced postdoc researchers are the main power in the biological labs in Europe. However, most bench work is done by the master and doctoral students. In this case, we need more time and effort to train the students.
Also, some labs in Europe are quite small – one PI tends to lead several postdocs and PhD students, although there are also big labs in Germany. In China, most labs, especially productive labs, are large!
How did you come to work in Professor Dong’s lab?
I met Professor Dong when we were in an EMBO symposium in Heidelberg, Germany in 2018. I was attracted by his work and also by his personality. We share similar scientific interests, and he asked whether I was willing to join to his group. Why not? It was a spontaneous decision.
You have been back in China for a couple of years now – what was it like coming home?
I have experienced ‘reverse culture shock’! For example, when we go to dinner with friends or colleagues, we do not split the bill in China. The leader or the senior person pays for all. As time passes, I will get used to Chinese culture again.
What question is your research currently trying to answer? The origin and the regulation of forces driving morphogenesis, and the crosstalk between genetic cascade and mechanical forces.
What are the main advantages and drawbacks of the model systems you work with, Drosophila and Ciona?
Some students in the lab often misunderstand that Drosophila is a user-friendly model compared to Ciona. The reason behind this might be that Drosophila is easier for genetic manipulation. But in my opinion, this is totally wrong – CRIPSR/Cas9 can also generate the mutant we want in Ciona. I think the advantage of Drosophila is that you can keep the stocks in the lab and you can do experiments whenever you want. The drawback of this model is that you have to take care the animals frequently. We need to collect Ciona from sea. So, the material is limited during early spring and late winter. We need to set up the inbred line in the lab. This is what we are currently doing. Ciona embryos and its larvae are smaller than Drosophila, which is a big advantage for imaging.
What is next for you?
I plan to focus more on Ciona embryogenesis research, and hope to involve myself in the Ciona community more actively.
Follow us on WeChat for exclusive interviews and research highlights written by the community, as well as useful resources to help navigate the publishing process.
Find out more about the Company’s efforts to engage with Chinese researchers
As the vertebrate body axis extends, HOX genes are sequentially activated in axial progenitors to specify their identity. A new paper in Development addresses what regulates the tempo of this HOX expression in human progenitors. To hear more about the story, we caught up with the paper’s two first authors, Vincent Mouilleau and Célia Vaslin, and their supervisor Stéphane Nedelec, Group Leader at the Institut du Fer à Moulin in Paris.
Vincent, Célia and Stéphane (L to R)
Stéphane, can you give us your scientific biography and the questions your lab is trying to answer?
SN: I studied Biology in Rennes and then Paris, where I did my PhD in the Department of Biology of the Ecole Normale Supérieure. I had the chance to work in the group of Alain Prochiantz under the supervision of Alain Trembleau, where I studied local protein synthesis in neurons. To follow up on this research I then joined Hynek Wichterle, who had recently started his lab at Columbia University. Hynek is a pioneer of in vitro differentiation of pluripotent stem cells (PSCs) to study development and diseases. It was very exciting to work in this environment in the early days of the field with great colleagues and so many things to explore, and this time at Columbia had a profound impact on my scientific career since I was still working on spinal cord development using in vitro approaches. I then moved back to France, working again in a very stimulating environment with Cécile Martinat at the I-STEM institute in Evry. There, I started projects aiming at studying human developmental biology using human PSCs (hPSCs). We developed a powerful approach to assess how extrinsic cues control cell fate and discovered pathways sufficient to convert hPSCs into distinct neuronal subtypes, including spinal motor neurons (MNs). Building on this work, I started a new lab in Paris, at the Institut du Fer à Moulin: a very dynamic and collaborative Neuroscience institute. The current story was largely developed there in collaboration with both the Hynek and Cécile groups, which was very satisfying.
We currently use spinal cord development as a model system to address two interrelated questions. First, the mechanisms by which a limited number of extrinsic factors control human spinal neuronal diversity and morphogenesis – in vitro differentiation of hPSCs is a unique model to approach this question. Second, the mechanisms by which mutations in ubiquitous genes perturb developmental programs to impair selective neuronal populations and cause MN diseases – here we take advantage of developmental studies to improve cell and tissue engineering.
Vincent and Célia – how did you come to work in Stéphane’s lab and what drives your research today?
VM: During my bachelor’s degree in Nantes I became fascinated by stem cells and neurodevelopment. I thus decided to join a Master’s program in Paris focusing on these two topics. The possibility of generating, in vitro, a specific subtype of human cells with the right ‘recipes’ fascinated me, and for my internship I joined the I-STEM institute and Stéphane’s lab. I then moved on to do a PhD, and helped Stéphane set up the new lab in Paris while continuing working between the two institutes. It was an intense but enriching experience.
CV: During my undergraduate studies at Sorbonne Université, I quickly became interested in developmental biology and neuroscience. During a first internship in the lab of Jean Livet in Paris, I studied neural lineages in the chick embryo spinal cord, which confirmed my interest in these two fields. This led me to join Stéphane’s lab, first as an intern and then a PhD student, to investigate molecular mechanisms controlling spinal cord development. The power of the in vitro approaches used in the lab allowed me to decipher signalling mechanisms controlling spinal neural diversification – a subject that fascinates me.
How has your research been affected by the COVID-19 pandemic?
VM, CV & SN: Our lab was completely shut down for 2 months last spring. Afterwards, we worked part-time on site to limit the number of people, which obviously significantly delayed the projects. However, working mostly with in vitro models helped, as it was easier to stop and restart the experiments. Also, the lockdown forced us to focus on writing and planning experiments, which was a positive side effect. Overall, this pandemic has most certainly delayed the progress of our research, but we were fortunate to return to the lab fairly quickly and be able to work in good conditions thanks to the heads of our institute, who did a fantastic job in dealing with the situation.
Before this project, what was understood about the relative influence of extrinsic and intrinsic factors on the pacing of the human HOX clock?
VM, CV & SN: We already knew a lot about the extrinsic and intrinsic mechanisms controlling the sequential induction of HOX genes during axial elongation. However, several aspects remain obscure; notably, the mechanisms pacing the clock within axial progenitors, in particular in humans. It was well established that cis-regulatory sequences within and outside the complexes are important for HOX gene sequential induction, and that progressive changes in chromatin structure along the complexes accompany the progression of the HOX clock. On the other hand, extrinsic factors such as retinoic acid (RA), Wnts, FGFs and GDF11 were shown to induce HOX gene collinear expression or modulate HOX gene expression patterns. However, whether these extrinsic factors were pacing the sequential activation within axial progenitors or were actuating an intrinsic timer was unclear.
Effects of modulating the duration of retinoic acid exposure on HOX gene expression during in vitro motor neuron differentiation.
Can you give us the key results of the paper in a paragraph?
VM, CV & SN: We first characterized the expression profile of HOX transcription factors and MN subtype markers in the human embryonic spinal cord, so we could assess the functional consequences of HOX regulation in axial progenitors and properly define the identity of in vitro-generated human MNs. Using MN subtype as a readout, as well as transcriptional analysis of the axial progenitor stages, we showed that HOX genes undergo a temporal collinear activation in hPSC-derived axial progenitors that, upon differentiation, generate MN subtypes found in progressively more caudal regions of the spinal cord. Analysis of the transcriptomic data showed that the sequential activation of HOX genes was paralleled by an increase in FGF ligands and markers of active FGF signalling. This FGF activity was necessary for the HOX clock to proceed, and precociously increasing FGF levels hastened the expression of HOX genes expressed normally later on. The HOX clock was further accelerated with a rapid rise of the very caudal HOX10 genes when FGF was combined with GDF11, another extrinsic factor known to control the expression pattern of caudal thoracic and lumbar HOX genes in mouse and chick embryos. Slowing down or accelerating the clock in axial progenitors was always paralleled by a shift in MN subtype specification within the same time line of differentiation. These results demonstrated that the pace of HOX gene activation within axial progenitors is regulated by sequences of extrinsic factors. This observation argues against a solely intrinsic, chromatin-based, pacing mechanism. However, even in the most accelerating/caudalizing conditions, HOX genes are still expressed in a largely collinear sequence, which suggests that cell-intrinsic mechanisms likely ensure the order of expression. In addition, our work provides for the first time a method to efficiently generate well-defined MN subtypes for basic and translation approaches.
The pace of HOX gene activation within axial progenitors is regulated by sequences of extrinsic factors
Do you have any idea what controls the onset and duration of FGF signalling in hPSC cultures and in the embryo?
VM, CV & SN: The onset and duration of FGF signalling in axial progenitors are certainly controlled by extrinsic factors both in vivo and in vitro. Work from different labs has indicated that FGF and Wnt signals, provided in vivo by the primitive streak and the surrounding epiblast, and in vitro by addition of agonists in the medium, specify axial progenitors, which in turn induce different FGF and Wnt ligands. Thereby, a positive-feedback loop is generated, which likely contributes to an increase in FGF signalling overtime. Accordingly, in this study we observed a temporal induction of FGF ligands and of well-recognized downstream target genes in hPSC-derived axial progenitors. Then, in the neuronal lineage, the duration of FGF signalling in axial progenitors depends on the rate of their differentiation in neural progenitors. In vivo, neurogenesis-promoting RA from the abutting somites can repress FGF gene expression and pathway activity. In our study, the duration of FGF signalling is also likely controlled by the moment at which axial progenitors are exposed to RA. Of note, we also showed that FGF concentration can be integrated by axial progenitors so, in addition to the duration of FGF signalling, a progressive increase in FGF concentration might play a role in pacing the HOX clock. Whether this occurs in embryos is currently unclear.
The dynamics of intracellular signalling downstream of FGFs might also play an important role in rostro-caudal patterning. We showed that FGF activity on HOX genes requires activation of the MAPK pathway. In other models, this pathway adopts distinct signalling activity dynamics in response to variations in concentration or in duration of extrinsic factors. Whether changes in intracellular signalling dynamics downstream of FGFs play a role in HOX clock regulation is an interesting avenue to pursue.
How do you think your findings will impact clinical or bioengineering efforts?
VM, CV & SN: It’s another important aspect of the paper. Studying developmental principles using hPSC differentiation helps optimize differentiation strategies so specific cell or tissues types can then be used for disease modelling, drug screening or cell therapy approaches.
In our case, one consequence of the discovery of the HOX pacing mechanisms is the ability to efficiently and synchronously generate MN subtypes found at different positions in the human spinal cord. MN diseases, such as amyotrophic lateral sclerosis or spinal muscular atrophies, differentially impact MN subpopulations, but the basis of this differential vulnerability remains largely unknown. Providing the community with the ability to generate these MN subtypes might stimulate research on these currently incurable diseases.
Finally, considering the iterative use of HOX transcription factors to induce cell diversity in many lineages, it will be interesting to explore whether our strategy could help refine the production of other cell types, such as somite or neural crest derivatives.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
VM: First seeing the efficient induction of caudal HOX genes while preserving MN induction was a particularly important moment. I’m also happy that we characterized HOX expression patterns and MN subtype markers in human embryos in collaboration with Gist and Mackenzie, who initiated that at Columbia. I think it will be an important resource.
CV: I tested different concentrations of Wnt agonist and I was particularly thrilled when I finally understood why a specific cell line required higher concentration of this agonist to generate caudal MNs. It’s a result that is a bit hidden in the manuscript but might have important consequences when people want to use these protocols with their favourite cell line. I also remember when I assembled images and graphs for the first time to organize the figures, I realized the accomplished work, even if much remained to be done at this time, and I was very proud of all the work we did together with Vincent.
And what about the flipside: any moments of frustration or despair?
CV: Experimentally, it has not always been smooth and easy: hPSCs can be tricky to deal with and are always demanding. However, I had the chance to work very closely with Vincent and constantly support each other, which helped a lot, both scientifically and personally. And finally, discovering such interesting results always cheered us up.
VM: As Celia said, working with hPSCs has its pros and cons as cells need to be taken care of almost every day, and all products and reagents need to be carefully calibrated. We had coating issues at some points and still unexplained cell death at another. These periods were very frustrating.
What next for you two after this paper?
CV: I am currently exploring the signalling mechanisms downstream FGF using reporters of signalling pathway activities. I will defend my thesis in a few weeks. Then I’m favouring a career in a biotech or industry.
VM: After defending my thesis I wanted to look for jobs abroad but the pandemic delayed this project. In the meantime, I’m helping with the national effort to test and track Covid patients while exploring future plans.
Where will this story take the Nedelec lab?
SN: On one hand, as we always try to combine developmental biology with cell engineering, we are exploring what’s downstream of the extrinsic factors that pace the HOX clock, the mechanisms by which they signal to the genome to induce distinct cell fates, and how they control spinal cord morphogenesis (using a new type of organoid model). 3D in vitro differentiation provides an experimentally accessible model for fine modulations of signalling pathways that can be coupled to genomic analysis while tracking consequences on cell fate and tissue shape. In collaboration, we are implementing optogenetic approaches and genomic approaches to address these questions.
On the other hand, we use the products of these developmental studies to study the basis of the differential vulnerability of MN subtypes in different forms of paediatric MN diseases called spinal muscular atrophies. For that, we have created a very stimulating network of collaborators, including clinicians and cell biologists.
Finally, let’s move outside the lab – what do you like to do in your spare time in Paris?
CV: A long time ago, before the pandemic, I really enjoyed living in Paris and often went to the cinema or museum, and I loved to discover new restaurants. But nowadays, it’s more biking or walking in the city and around, when the weather is nice!
VM: I like to walk randomly and get lost in the maze of Paris, discovering new streets and monuments randomly. When it was still possible, I particularly enjoyed waking up early on weekends to go to the Louvre to walk around the museum with almost nobody around. I also really enjoyed going to bars with co-workers to share problems and discuss projects. While I reduced this activity during my PhD, I’m also a big fan of Aikido.
SN: As Célia and Vincent mentioned, Paris will, hopefully, soon be Paris again, so we can enjoy the theatres, museums and the terraces. I also like rock climbing and, while it might sound surprising, Paris is not such a bad place for it. The nearby forest of Fontainebleau is a fantastic bouldering spot with endless possibilities. As my daughter has started to really enjoy it as well, I try to go as much as I can.
The immune system is able to deal with cellular anomalies and invading pathogens. However, it has remained enigmatic how vertebrate embryos handle stress conditions before such an immune system develops. We recently found that embryos are able to perform innate immune functions as early as in blastula stage of development, using the surface epithelium as a phagocytic clearance system of defective cells1. This epithelium, the trophoblast in mammalian embryos, is the first differentiated tissue that forms during embryonic development, and our study revealed that it has unrecognized important functions for the survival of the early embryo.
The story began when Esteban joined as a postdoctoral researcher the recently established lab of Verena at the Centre for Genomic Regulation in Barcelona, Spain. With the aim to study early vertebrate embryo development under native and stress conditions we started to acquire movies of single cell dynamics at high spatiotemporal resolution in the zebrafish blastula. Interestingly, we noticed that epithelial cells of the embryo surface (termed enveloping layer in zebrafish) were able to ingest fragments of internal stem cells, forming vacuolar like structures in epithelial cells (Figure 1). We further observed that epithelial uptake was specifically increased in stressed embryos that showed signs of malformations or tissue damage caused by mechanical perturbation, suggesting that the ingested cells originated from cellular failures or events of cell death. In fact, we were able to confirm that the surface epithelium specifically ingested dead cells, as the ones generated in normal embryo development by errors in mitosis. This led us to think that the epithelial tissue at the embryo surface formed during early development (only four hours post fertilization in zebrafish embryos), could function as a scavenger of dead cells at these stages. This was a challenging idea, as specific clearance functions of epithelial cells have not been previously considered to occur in the early embryo. Phagocytosis of dead cells by epithelia was known to be important in certain adult tissues2-3, suggesting that epithelial cells could perform similar functions in the early embryo. We reasoned that this function could have an essential protective role in development, as an accumulation of dead bodies might lead to multiple defects, from mechanical interference with gastrulation movements to the uncontrolled release of intracellular contents by secondary necrosis, including signaling molecules and toxic factors.
Motivated by the possible relevance of these observations, Esteban combined his expertise in live embryo imaging with experience in cell apoptosis that he gained during his PhD. We developed a single cell in vivo morphodynamic analysis of phagocytosis that allowed us to study epithelial phagocytic events inside a living animal (Figure 1B). Our study revealed that the phagocytic cup formed by epithelial cells exerts compressive forces during uptake of an apoptotic cell, a feature recently discovered to be shared by macrophages ingesting synthetic phagocytic targets in culture4.
Next, we decided to evaluate if this process was conserved in mammals, as this could have relevant implications for the progression of human embryonic development. Filming mouse blastocysts, we observed that the surface epithelium (in this case the trophoblast) was also able to clear apoptotic cells by recognizing surface molecules of dying cells, specifically phosphatidylserine. This observation indicated that the early epithelial phagocytic process we first observed in zebrafish embryos was evolutionary conserved and based on similar molecular mechanisms to the ones used by professional phagocytic cells of the immune system such as macrophages. These results were exciting, as they suggested that the first tissue formed at the surface of a vertebrate embryo is used for its protection. This is particularly relevant considering that the main cause of early miscarriages in human embryos are errors in mitosis leading to cell death5.
We observed that phagocytic clearance was sensitive enough to detect single cells dying, while being efficient enough to be able to clear hundreds of cells dying simultaneously (Figure 1). We were thus wondering how epithelial cells, which are sessile cells in the epithelium, can achieve such high efficiency for clearance, as compared to immune phagocytes which are motile to perform their (clearance) task. The answer was hidden in our movies of live zebrafish embryos. We detected two surprising features: first, dead cells moved much more than what we expected before the uptake, significantly faster than the live neighboring cells undergoing gastrulation movements. Although it was proposed that apoptotic cells can acquire specific motility inside tissues, this was not directly proven to be cell-autonomous6-8. Our dynamic analysis of actomyosin network organization, which showed a static localization and non-polarized organization in apoptotic cells, was however supporting that they do not have autonomous motility. Second, by visualizing F-actin dynamics inside the whole embryo, we observed the formation of actin accumulations in contact with the external rear surface of motile apoptotic cells. We therefore questioned, could these two observations be linked? Surprised by the observation of these actin structures, we performed both high-speed imaging to analyze actin localization dynamics and single cell staining to identify the cells in which they are formed. This allowed us to determine that these actin structures formed in epithelial cells and constitute a new elongated protrusion, with actin enriched at the protrusion tip in contact with apoptotic cells and moving coordinately with them, a protrusion type that we called “epithelial arms” (Figure 2A,B).
Figure 2. Epithelial arms propel apoptotic cells improving tissue clearance efficiency. (A) An epithelial arm forms upon contacting an apoptotic cell (red). (B) Epithelial cells form two types of protrusions when recognize an apoptotic cell: phagocytic cups to ingest and epithelial arms to push. (C) Consecutive pushing by epithelial arms increases the number of epithelial cells encountered by the each apoptotic cell (red). (D) Modeling indicates that the time to complete clearance of an apoptotic mass is reduced when velocity of the apoptotic targets increases. Nmax: maximum number of targets ingested by each epithelial cell. Adapted from Hoijman et al, Nature 2021, 590:618.
We came up with different hypotheses that might explain this observation: Could these protrusions mechanically push the apoptotic cells? Or are protrusions just “chasing” apoptotic cells? In the latter case, we should probably observe some apoptotic cells moving without contacting epithelial arms. However, we observed a stringent correlation between arms and apoptotic movement with both occurring hand in hand. To evaluate our first hypothesis, we designed an experiment in which we transplanted synthetic apoptotic targets made of lipid aggregates into the embryo as a source of objects with no intrinsic motility. Interestingly, these targets were efficiently phagocytosed and, furthermore, they acquired similar motility as apoptotic cells in terms of velocity fluctuations, directionality, and association with epithelial arms. The movement of the surrogate targets indicated that epithelial arms can propel apoptotic targets using actin-dependent forces. Looking at the whole tissue, we further found that apoptotic cells moved along long-range trajectories, caused via consecutive pushing by multiple epithelial arms formed by different epithelial cells (Figure 2C), with the path for each dead cell target being described by a random-walk.
We therefore asked, how does this apoptotic target movement influence the overall efficiency of tissue clearance? In other words, from the point of view of a single epithelial cell, why would it be meaningful to push a target instead of ingesting it directly? Analyzing population movement of apoptotic targets, we observed that the random-walk behavior led to the overall spreading of the apoptotic mass. A larger area of the epithelial tissue was therefore “visited” by apoptotic targets over time. Comparing this behavior to professional phagocytes, which usually move towards an apoptotic cell mass to perform efficient clearance, we interpreted the observed spreading of the apoptotic mass as an inversion of the clearance process, with motile targets moving around sessile epithelial phagocytes.
The immediate consequence of apoptotic motility was an increased number of epithelial cells encountered by each target. We hypothesized that several possibilities could lead to an advantage for cells clearing the tissue when increasing the phagocyte-target encounter rate. We therefore set out to mathematically model the clearance process and its efficiency. For this, Verena teamed up with Stefan Wieser (ICFO Barcelona) and Andrew Callan-Jones (CNRS/Université de Paris) to perform simulations and derived a theoretical formula that predicted that increasing the speed of target spreading (mediated by arm pushing) decreases the time required to clear the whole apoptotic mass, thus making the process more efficient (Figure 2D). Importantly, this was specifically relevant when a limited uptake capacity for each epithelial cell exists, as we determined experimentally.
The successful combination of this theoretical and experimental analysis indicated that the stochastic spreading allows the recruitment of new epithelial phagocytes near the vicinity of those cells that already reached their maximal uptake capacity, thereby accelerating the clearance process at the tissue level.
In summary, the mechanical cooperation between epithelial cells mediated by the active dispersal of apoptotic targets by epithelial arms improves the protection of the embryo at the earliest stages of development. We are now exploring the impact of this phagocytic system at the CRG Barcelona (Verena) and the newly established group at the University of Barcelona (Esteban).
As many other researchers experienced in 2020-2021, performing a revision in the peak of the pandemic was a challenging situation that led us to deal with complex situations and demanded creative solutions and support between labs to solve unpredictable problems (i.e. we needed a reagent during the revision when companies paused their supply; we were lucky to receive it as a gift from the lab next door). We believe that our work is a good example of how advanced imaging technologies that can nowadays capture single cell and molecular dynamics inside live animals open new exciting opportunities for the discovery of relevant in vivo cell and tissue functions and their underlying mechanisms.
In the latest episode of the Genetics Unzipped podcast we’re meeting some of the researchers who are working to make sure that everyone gets the benefits of genetic research – from underserved communities to entire continents.
Kat Arney chats with Charles Rotimi, director of the Centre for Genomics and Global Health within the NIH National Human Genome Research Institute at Bethesda, Maryland in the US, and a distinguished NIH investigator. He’s also the founder of the African Society of Human Genetics and the driving force behind a major genomics project called Human Heredity and Health in Africa, or H3Africa, which he helped to establish ten years ago.
She also talks with Laura Koehly – a senior investigator at the National Human Genome Research Institute, with a special interest in helping people unlock the information hidden in their family health histories, particularly focusing on underserved and less privileged communities.
Finally, Kat hears from bioethicist Sara Hull, who has worked at the National Institutes of Health for more than 20 years helping researchers make sure their work is done ethically and doesn’t cause harm to the people involved.
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
Cell migration needs to be precisely regulated during development so that cells stop in the right position. A new paper in Development investigates the robustness of neuroblast migration in the C. elegans larva in the face of both genetic and environmental variation. To hear more about the story, we met the paper’s four authors: Clément Dubois and Shivam Gupta, and their respective supervisors Andrew Mugler (currently Assistant Professor at the Department of Physics and Astronomy at the University of Pittsburgh, where his lab recently moved from Purdue University) and Marie-Anne Félix (Principal Investigator at Institut de Biologie de l’Ecole Normale Supérieure in Paris and Research Director at CNRS).
Clément (top left), Shivam Gupta (top right), Marie-Anne (bottom left) and Andrew (bottom right).
Andrew and Marie-Anne, can you give us your scientific biographies and the questions your labs are trying to answer?
AM: After a PhD and postdoctoral research on theoretical biological physics, I began my own position investigating noise in biological systems. Cells contend with unavoidable noise from environmental fluctuations, small molecule numbers and many other sources. My group uses tools from theoretical physics to uncover strategies that cells use to precisely sense their environment, undergo controlled developmental or phenotypic changes, and execute collective behaviours.
M-AF: After a PhD in cell biology, I wanted to combine evolutionary biology with cell/developmental biology. In Paul Sternberg’s lab at Caltech and in my lab’s early years, we compared vulva development in different nematode species, giving flesh to the concept of developmental systems drift. Over the past 20 years, we moved to a microevolutionary scale: studying the sensitivities of developmental systems to various types of perturbation and comparing these with their evolutionary variation. The overall thread is to assess how much development biases phenotypic evolution, with some phenotypes being more easily reached than others upon random genetic variation or quantitative tuning of parameters.
Studying natural variation led us to seek C. elegans in nature, which was a lot of fun. With many colleagues, we have since been probing its population genetics structure, and the zoo of its associated microbes. Bringing real worms back to the lab also led us to discover natural variation in the duration of their multigenerational memory.
Clément and Shivam – how did you come to work in your respective labs and what drives your research today?
CD: I did an MSc in ecology and evolution, and was specifically interested in host-pathogen interactions. After a first internship in the Pasteur Institute working on mosquito-virus interactions, my former supervisor suggested I apply to Marie-Anne’s lab. I started working on the intraspecific evolution of C. elegans resistance to microsporidia, and then did a year as a technician working on the evolution of a peculiar cell in C. elegans called P3.p. This year was really formative. I gained a lot of scientific maturity, and realised how rich and friendly the C. elegans community is. Then Marie-Anne proposed I do a PhD on the evolution of QR neuroblast migration. Considering the different topics I worked on, I would say that my research is mostly driven by curiosity and the question of how much genotypes can shape phenotypes.
SG: I came to Purdue University as a grad student in 2015. I joined Dr Mugler’s lab after doing a lab rotation to get a feel for the research. The research work in the Mugler lab was very challenging, and it was intriguing to see how fundamental physics can explain the behaviours of microscopic organisms.
How has your research been affected by the COVID-19 pandemic?
M-AF: The lab closed for 3 months in the spring of 2020; since then it has been somewhat restricted, but we can do experiments. Of course, C. elegans is a great organism to work on because we do not lose strains: they can be kept frozen or can live for 3 months in diapause (a pre-adaptation to SARS-CoV2!). But some projects were affected for more than 3 months. To enhance social interactions, since the fall we decided to meet after lunch every day in a hybrid format (real life and video). This compensates for the usual lunch-time exchanges, be they scientific or not. On the positive side, the pandemic also gave us the impetus to meet more readily with colleagues worldwide, attending each other’s lab meetings or organising informal meetings.
AM: As a theory group, we could continue most of our work from home without interruption. However, developing ideas in any area benefits from true collective brainstorming, which has been slowed without the ability to physically meet at the whiteboard. Additionally, the pandemic has increased my childcare responsibilities, which has left less time to dedicate to students. On the positive side, I moved institutions in the middle of the pandemic, and I now hold hybrid group meetings with group members from both places, which is perfectly natural to do virtually in these times.
How did your labs come to collaborate on this project?
AM & M-AF: This was all started by our colleague Rik Korswagen, who has been working on C. elegans QR migration as a model. He contacted us both to write an application for a collaborative grant from the Human Frontier Science Program. We got the grant, and this has been a great experience. The modelling of body size variation was not in the grant, but the collaboration took place naturally once we were networking.
Can you give us the key results of the paper in a paragraph?
CD, SG, AM & M-AF: The goal was to measure the precision and natural variation in the final position of a cell that migrates during development. Other studies in various systems have examined the directionality of cell migration, but to our knowledge not the precision in the cell’s final position. Specifically, we studied two descendants of the QR neuroblast lineage that migrate a long way during C. elegans development. The Korswagen lab had shown that the end of their migration is specified by a temporal rather than a spatial mechanism. Given this temporal regulation, we hypothesised that a change in body size would affect the final position of the neurons relative to body landmarks. Indeed, we observed that a smaller body size resulted in the cell migrating further. Cell position even changed as a function of maternal age, a factor previously known to affect body size. We developed a mathematical model of the expectation, taking into account larval growth during the migration. The data did not fit quantitatively the simplest form of the model. Then, a model with partial compensation of body size, grounded on measurements of cell speed, fitted the experimental results without any free parameters. Finally, we revealed natural variation among wild isolates of C. elegans in the neurons’ final position, large enough that they result in a change in their neighbouring cells.
Late L1 larvae showing examples of the relative position of QR.pax in different strains: posterior (strain XZ1516, top) and anterior (strain EG4725, bottom).
Do you have any idea why cell migration speed is dependent on body size?
CD & M-AF: The first that comes to mind is that a larger body size means larger cells (at least for a species such as C. elegans, which has a quasi-invariant number of cells). But interestingly, we could not find much published on whether a larger cell would go faster or slower than a smaller one. Both appear possible, depending on specific motility mechanisms. Another possibility is that the external environment of the cell is altered as a function of body size; for example, a change in the Wnt gradient that influences QR migration, either its initial concentration or its decay length.
On the other hand, in the wild isolates, the eventual position of QR.pax did not correlate with body size: why do you think this is?
CD & M-AF: We did not detect a significant correlation, and we cannot rule there would be one with a larger set of experiments. In any case, this means that much of the variation is due to other factors that can go in another direction than the effect of body size. Variation in many genes and processes can affect a quantitative trait such as cell position.
Your paper was published in Development through the Review Commons route – how did you find the experience?
CD, SG, AM & M-AF: Great! This was our first time. With Review Commons, the manuscript is sent to reviewers without any submission to a specific journal. The reviewers do not have any specific journal in mind. In our case, the reviews were very constructive, especially by suggesting that we assessed the effect of maternal age. Once the reviews arrived, the authors can contact one of the participating journals, specifying what is planned for responding to reviews. Thanks to Development, this went very well.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
CD: The first eureka moment was to see the preliminary results on the natural variation of QR.pax final position. To be able to detect differences between wild isolates for the first time was really exciting and promising. From then on, I was excited at the end of each experiment after making plots from the data (and I spent a lot of time on them!).
SG: The first few months of my PhD work was mainly building mathematical models for temporal precision in gene expression. At first, I was a bit pessimistic that the rules of physics would explain the complex behaviour of organisms. After analysing experimental data from C. elegans, it was very satisfying to see that the behaviour of microscopic cells can be explained by our models.
And what about the flipside: any moments of frustration or despair?
CD: I did not have a particularly memorable moment of frustration or despair – even negative results were informative. Nonetheless, the most challenging part was probably the measurements of embryo and larva lengths at different time points, in parallel on four genotypes. It required a lot of organisation and efficacy, but it was worth it.
SG: To solve complex biological problems, we start with a simple model and slowly build up the model. After a point, our model became very complex and it took days to run the computer program. It was frustrating to wait days to see results, but in the end, when results were promising, it was very joyful.
What next for you two after this paper?
CD: In the short term I’m doing two things: writing my PhD manuscript and working on the intraspecific evolution of the final position of QR.pax. Using Recombinant Inbred Lines between CB4932 and JU1242 (two genotypes with an opposite phenotype), I found a QTL on chromosome IV. The goal now is to find the polymorphism associated with the difference in QR.pax final position.
SG: I have successfully defended my thesis and secured a job in the pharmaceutical industry. My ambition is to advance drug discovery and safety of drugs through developing pharmacokinetics/pharmacodynamics models and analysing clinical trial data.
Simple mathematical models can prove very useful for sharpening basic understanding of biological systems
Where will this story take the Mugler and Félix labs?
AM: This has been one of the most positive demonstrations that simple mathematical models can prove very useful for sharpening basic understanding of biological systems; I hope to continue in this vein with this and other collaborations.
M-AF: I hope we can find the polymorphism behind the divergent phenotypes of two wild C. elegans isolates. Beyond, I will keep vulva development as our main developmental model, but, as both are regulated by the same Wnt gradient, we will likely come back again to QR migration.
Finally, let’s move outside the lab – what do you like to do in your spare time in Paris and West Lafayette?
CD: Paris is full of small and hidden restaurants that are really good. I like to explore them with my partner. I also enjoy spending time with my friends playing board games, climbing in the gym or in Fontainebleau, a forest close to Paris known for its large boulders.
SG: I enjoy exploring new places around West Lafayette for hiking and biking.
AM: Biking, exploring new restaurants and travelling.
Hello! Welcome back to the #devbiolwriteclub! Over the last year or so, I’ve harangued you on Twitter and on The Node about practicing the craft of writing. I’ve ignored any practical advice on what you should actually put on a page and instead I have focused on how to build the habits of mind that allow you to grow as a writer. Yesterday, I launched a new Twitter project called #devbiolgrantclub, where I’ll be offering random bits of grantsmithing advice. Today, I’ll present a “crossover episode” of the two projects.
As academic scientists, we all know that we must master two types of writing: papers and grants. But I don’t think enough people really grasp the fact that the two represent entirely distinct disciplines within scientific writing. In fact, the best way to write a grant is totally, totally different from the best way to write a paper.
Ask anyone in my lab, and they’ll tell you that I love papers like druids love trees. Writing papers is one my life’s greatest joys. It’s also the ultimate goal of science, which is why papers are the hard currency of our field. In fact, call me sentimental, but I see something noble in our endeavor to elegantly reveal to the world the new knowledge that we have discovered.
Just the same, doing this noble work while simultaneously contemplating my next grant proposal brings to mind a great Melvern Taylor song, from which I borrowed this post’s title. That angel is perched there on your shoulder, egging you on as you do the good work of science. But let me tell you, successful grant writing absolutely requires that you ignore that angel and listen very carefully to the devil on your other shoulder.
The best grant writing advice I ever heard came from a clinician from UT, San Antonio at a grant writing workshop I attended when I was in Berkeley as a postdoc. Between solid practical advice and a riotously funny story about tequila and a big stack of grants to review, he said this:
“Listen. You don’t have to be proud of what you wrote. You have to get the money.”
Think about that. Let it sink in. It’s harsh, for sure. It may even be antithetical to how we see ourselves as academic writers. But it’s the ultimate truth of grant writing. You don’t have to be proud of what you wrote. You just have to get the money.
Now let me be clear: I am not talking about being sleezy or self-aggrandizing, and I’m definitely not talking about making stuff up. Rather, I am simply proposing that you be intentional about grant writing by ignoring what you want, learning exactly what your audience needs, and providing exactly that.
To understand what I mean, consider this: Every once in a while, I find myself with a totally free afternoon. So, what do I do? I go get a cup of coffee, sit somewhere pleasant, and read papers. Maybe I grab a few from the stack on my desk, maybe I hit Pubmed to look for something new, or maybe I click a link on Twitter. It’s a joy.
On the other hand, no one in the history of science ever said to themselves: “Gee, I’d really like to read and carefully review ten randomly assigned grants in my free time today.” This gives us the First Principle of grant writing:
1. Assume your readers do NOT want to read your grant.
This is possibly the biggest concept that grant writers fail to grasp. When you write a paper, you can reasonably assume that whoever reads it wants to read it. They very likely share your interest in the subject. You might even say they want to know how the story ends. Thus, they are actually quite likely to overlook a confusing paragraph, or power through a difficult passage. At the very least, they’ll give it a read and likely learn something.
But your reviewer did not choose to read your grant. Your reviewer was assigned your grant by a grant officer. The cynical (and effective) grant writer therefore assumes that the reviewer does not care how the story ends, but does know exactly when it will end: When the review is written and submitted to that grant officer.
Presented with this hard fact, you might feel compelled to try to write the grant in such way as to MAKE the reviewer want to read the grant. Don’t. It’s too risky. There are just too many variables. (E.g., Sorry, you cannot ever make me want to read a grant about… well, lots of things, but I won’t name them.)
On the other hand, there is one thing that will make all reviewers happy, and that is making the grant EASY for the reviewer to read and absorb. More thoughts on how to do this later, but for now, let me drive home why this strategy works by presenting the Second Principle of grant writing:
2. Accept that your readers MUST compare your grant to other grants, mentally ranking them in real time.
This is another critical distinction between grants and papers that people usually don’t consider when writing. If I am doing my work as a scientist, I am judging the quality of every single paper. Am I convinced by the data? Do I care about the conclusions? Just the same, I am not sitting there thinking hard about whether your paper is better or worse than the last one I read. And I am absolutely not trying to mentally rank the last ten papers I read. On the other hand, if I am reading your grant, this is exactly what I am doing.
This simple fact creates a very different workflow for grant readers, as compared to paper readers. The grant reader won’t just start reading ten grants in the order they were assigned. Instead, most reviewers will at least glance through the grants they are assigned, but then will pretty quickly decide which ones to read first – or last. So, in very short order, a mental ranking of some sort is already starting to emerge. This bears directly on our work as grant writers.
Here’s another thought exercise. You are a reviewer with a stack of nine grants. Two are in your specific sub-field and are asking questions that you find interesting. One grant has the minimum-allowed 0.5-inch margins, long paragraphs taking up nearly half a page, no white space breaking up the text, tables filled with huge amounts of data in small fonts, and no color anywhere. The other grant has larger margins and bullet points and colorful diagrams to summarize key points; these are well separated by white space from the main text, and that text is presented in short, easy-to-digest paragraphs. This second grant stops several inches short of the bottom of that last page. Tell me, which of those two grants -that you have to read today- will you choose to read first?
This brings us to the Third Principle.
3. Help your readers; they have to WRITE a careful review of your grant, AND ALSO several other grants.
This is the last major distinction between paper and grant readers. When I am reading a paper, I may or may not need to write about it, but if I do, I will usually end up doing so in a pretty indirect way. I’m very unlikely to do that writing the same day I read the paper. But consider the beleaguered grant reviewer. Just a few weeks to read an entire stack of grants, choose which ones are better and worse, and write reviews for all of them, justifying their decisions.
So, as a writer, this is where I am least proud of my grant writing: In my quest to make my grants easy for Reviewers, I consider that there are sections of NIH grant review forms titled Significance and Innovation. So, my grants include prominent, underlined sentences that read: “This grant is significant because…” or “This grant is innovative because…”. It’s clunky, unsubtle language, and I hate it. I hate bullet points, too. I also despise witless diagrams that I know are oversimplified. But if I provide these things, and do so with care and intent, it will help me get the money.
So those are three Principles to keep in mind when writing grants. Next, let’s see how they relate to the Rules of #devbiolwriteclub.
Rules #1 and #2 tell us to do the work. Make grant writing a specific craft you practice with intent throughout your career, not just this thing you need to do when you’re out of money.
Rule #3 tells us to revise and edit, again and again. When you are doing this, though, keep the Principles foremost in your mind. Revise and edit to make the grant EASIER to read, EASIER to rank, and EASIER to review.
Rule #4 tells us to read with intent. So, read grants with intent. Ask you PI and your peers for grants they wrote. Read the ones that got funded, but also read the ones that DID NOT get funded. Read the reviews! Here’s an idea I just came up with: Instead of journal club, have grant reviews club. Read a grant and the reviews together as a group. Try to figure it out.
Rule #5 says you can’t do it alone. So, when you beg your friends to read your grant, don’t ask them if they found typos. Ask them if it was easy to read. Also, recall that grants are assigned to reviewers, frequently outside their core area. So, ask people WHO ARE NOT IN YOUR lab to read your grants.
Finally, leave waxing lyrical and fighting the good fight for your papers.
Write grants with a singularity of purpose: Get the Money.
Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway Hyae Yon Kweon, Mi-Ni Lee, Max Dörfel, Seungwoon Seo, Leah Gottlieb, Thomas Papazyan, Nina McTiernan, Rasmus Ree, David Bolton, Andrew Garcia, Michael Flory, Jonathan Crain, Alison Sebold, Scott Lyons, Ahmed Ismail, Elaine Marchi, Seong-keun Sonn, Se-Jin Jeong, Sejin Jeon, Shinyeong Ju, Simon J. Conway, TaeSoo Kim, Hyun-Seok Kim, Cheolju Lee, Tae-Young Roh, Thomas Arnesen, Ronen Marmorstein, Goo Taeg Oh, Gholson J. Lyon
Preterm birth alters the development of cortical microstructure and morphology at term-equivalent age Ralica Dimitrova, Maximilian Pietsch, Judit Ciarrusta, Sean P. Fitzgibbon, Logan Z. J. Williams, Daan Christiaens, Lucilio Cordero-Grande, Dafnis Batalle, Antonios Makropoulos, Andreas Schuh, Anthony N. Price, Jana Hutter, Rui PAG Teixeira, Emer Hughes, Andrew Chew, Shona Falconer, Olivia Carney, Alexia Egloff, J-Donald Tournier, Grainne McAlonan, Mary A. Rutherford, Serena J. Counsell, Emma C. Robinson, Joseph V. Hajnal, Daniel Rueckert, A. David Edwards, Jonathan O’Muircheartaigh
Connectomes across development reveal principles of brain maturation Daniel Witvliet, Ben Mulcahy, James K. Mitchell, Yaron Meirovitch, Daniel R. Berger, Yuelong Wu, Yufang Liu, Wan Xian Koh, Rajeev Parvathala, Douglas Holmyard, Richard L. Schalek, Nir Shavit, Andrew D. Chisholm, Jeff W. Lichtman, Aravinthan D.T. Samuel, Mei Zhen
A comprehensive series of temporal transcription factors in the fly visual system Nikolaos Konstantinides, Anthony M. Rossi, Aristides Escobar, Liébaut Dudragne, Yen-Chung Chen, Thinh Tran, Azalia Martinez Jaimes, Mehmet Neset Özel, Félix Simon, Zhiping Shao, Nadejda M. Tsankova, John F. Fullard, Uwe Walldorf, Panos Roussos, Claude Desplan
A multimodal iPSC platform for cystic fibrosis drug testing Andrew Berical, Rhianna E. Lee, Junjie Lu, Mary Lou Beermann, Jake A. LeSeur, Aditya Mithal, Dylan Thomas, Nicole Ranallo, Megan Peasley, Alex Stuffer, Jan Harrington, Kevin Coote, Killian Hurley, Paul McNally, Gustavo Mostovslavsky, John Mahoney, Scott H. Randell, Finn J. Hawkins
Stem cell-free therapy for glaucoma to preserve vision Ajay Kumar, Xiong Siqi, Minwen Zhou, Wen Chen, Enzhi Yang, Andrew Price, Liang Le, Ying Zhang, Laurence Florens, Michael Washburn, Akshay Kumar, Yunshu Li, Yi Xu, Kira Lathrop, Katherine Davoli, Yuanyuan Chen, Joel S. Schuman, Ting Xie, Yiqin Du
Zebrafish pigment cells develop directly from persistent highly multipotent progenitors Masataka Nikaido, Tatiana Subkhankulova, Leonid A. Uroshlev, Artem J. Kasianov, Karen Camargo Sosa, Gemma Bavister, Xueyan Yang, Frederico S. L. M. Rodrigues, Thomas J. Carney, Hartmut Schwetlick, Jonathan H.P. Dawes, Andrea Rocco, Vsevelod Makeev, Robert N. Kelsh
Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome Laura Jardine, Simone Webb, Issac Goh, Mariana Quiroga Londoño, Gary Reynolds, Michael Mather, Bayanne Olabi, Emily Stephenson, Rachel A. Botting, Dave Horsfall, Justin Engelbert, Daniel Maunder, Nicole Mende, Caitlin Murnane, Emma Dann, Jim McGrath, Hamish King, Iwo Kucinski, Rachel Queen, Christopher D Carey, Caroline Shrubsole, Elizabeth Poyner, Meghan Acres, Claire Jones, Thomas Ness, Rowan Coulthard, Natalina Elliott, Sorcha O’Byrne, Myriam L. R. Haltalli, John E Lawrence, Steven Lisgo, Petra Balogh, Kerstin B Meyer, Elena Prigmore, Kirsty Ambridge, Mika Sarkin Jain, Mirjana Efremova, Keir Pickard, Thomas Creasey, Jaume Bacardit, Deborah Henderson, Jonathan Coxhead, Andrew Filby, Rafiqul Hussain, David Dixon, David McDonald, Dorin-Mirel Popescu, Monika S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Aviv Regev, Sam Behjati, Elisa Laurenti, Nicola K. Wilson, Anindita Roy, Berthold Göttgens, Irene Roberts, Sarah A. Teichmann, Muzlifah Haniffa
Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates Andrea Toth, Shelby Steinmeyer, Paranthaman Kannan, Jerilyn Gray, Courtney M. Jackson, Shibabrata Mukherjee, Martin Demmert, Joshua R. Sheak, Daniel Benson, Joe Kitzmiller, Joseph A. Wayman, Pietro Presicce, Christopher Cates, Rhea Rubin, Kashish Chetal, Yina Du, Yifei Miao, Mingxia Gu, Minzhe Guo, Vladimir V. Kalinichenko, Suhas G. Kallapur, Emily R. Miraldi, Yan Xu, Daniel Swarr, Ian Lewkowich, Nathan Salomonis, Lisa Miller, Jennifer S. Sucre, Jeffrey A. Whitsett, Claire A. Chougnet, Alan H. Jobe, Hitesh Deshmukh, William J. Zacharias
A mechano-osmotic feedback couples cell volume to the rate of cell deformation Larisa Venkova, Amit Singh Vishen, Sergio Lembo, Nishit Srivastava, Baptiste Duchamp, Artur Ruppel, Stéphane Vassilopoulos, Alexandre Deslys, Juan Manuel Garcia Arcos, Alba Diz-Muñoz, Martial Balland, Jean-François Joanny, Damien Cuvelier, Pierre Sens, Matthieu Piel
A ciliopathy complex builds distal appendages to initiate ciliogenesis Dhivya Kumar, Addison Rains, Vicente Herranz-Pérez, Quanlong Lu, Xiaoyu Shi, Danielle L. Swaney, Erica Stevenson, Nevan J. Krogan, Bo Huang, Christopher Westlake, Jose Manuel Garcia-Verdugo, Bradley Yoder, Jeremy F. Reiter
Mouse oocytes do not contain a Balbiani body Laasya Dhandapani, Marion C. Salzer, Juan M. Duran, Gabriele Zaffagnini, Cristian De Guirior, Maria Angeles Martínez-Zamora, Elvan Böke
Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes Jeremy Vicencio, Carlos Sánchez-Bolaños, Ismael Moreno-Sánchez, David Brena, Dmytro Kukhtar, Miguel Ruiz-López, Mariona Cots-Ponjoan, Charles E. Vejnar, Alejandro Rubio, Natalia Rodrigo Melero, Carlo Carolis, Antonio J. Pérez-Pulido, Antonio J. Giráldez, Benjamin P. Kleinstiver, Julián Cerón, Miguel A. Moreno-Mateos
Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A. Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A. Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A. Longacre, John Hickey, Yiing Lin, M. Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J. Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T. Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, Griffin Weber
A dynamic pattern of histone methylation and demethylation controls gene expression during development, with some processes such as formation of the zygote involving large-scale reprogramming of methylation states. A new paper in Development investigates how inherited histone methylation regulates developmental timing and the germline/soma distinction in Caenorhabditis elegans. To hear more about the story we caught up with first author and postdoctoral researcher Brandon Carpenter, and his supervisor David Katz, Associate Professor in the Department of Cell Biology at Emory University School of Medicine in Atlanta, Georgia.
Brandon (L) and David (R)
David, can you give us your scientific biography and the questions your lab is trying to answer?
DK: As a graduate student, I worked with Dr Shirley Tilghman at Princeton on the regulation of genomic imprinting. We provided in vivo evidence for the first chromatin boundary formed by CTCF at the H19 locus in mouse. As a postdoc, I worked for Dr Bill Kelly at Emory University on the regulation of histone methylation in the germline of C. elegans. We provided the first evidence of a transgenerational phenotype (sterility) caused by the build-up of histone methylation, when the H3K4me1/2 demethylase Lsd1 is mutated. In my own lab at the Emory University School of Medicine, we have worked on both C. elegans and mouse model systems to study the mechanisms that regulate histone methylation and how inappropriately inherited histone methylation gives rise to phenotypes. We have also implicated LSD1 as a crucial molecule that may contribute to Alzheimer’s disease: our data suggest it is being inhibited by pathological aggregates in dementia patients. We are currently trying to develop a therapeutic intervention based on what we have learned about the function of LSD1 in the Alzheimer’s disease pathway.
Brandon – how did you come to work in David’s lab and what drives your research today?
BC: After obtaining my doctoral degree, I knew I wanted to continue studying development, and that I wanted to focus on a model system that would allow undergraduates to develop projects related to my research. As a graduate student, I fell in love with mentoring students and wanted to find opportunities to inspire students in the classroom as well as at the bench. Thus, my passion for mentoring and studying developmental biology led me to the Katz lab, where I could work with the beautiful model system, C. elegans, to study how epigenetic inheritance affects developmental cell fates.
At Emory University, I joined the Katz lab as a Fellowship In Research and Science Teaching (FIRST) Fellow (part of the National Institutes of Health-funded IRACDA programme) where, in parallel with my research, I was able to develop my teaching and mentorship skills. The most exciting part of joining the Katz lab was being able to bring my research into the classroom at Oglethorpe University, a nearby small liberal arts college. The Katz lab has a longstanding collaboration with Dr Karen Schmeichel from the biology department at Oglethorpe, integrating C. elegans experiments into the entire curriculum. As part of this, I was able to teach a semester-long Course-based Undergraduate Research Experience (CURE) based on the research I was conducting in the Katz lab. As part of this semester-long CURE, Oglethorpe students became inspired by the science we are doing in the Katz Lab and generated data for this manuscript. Jovan Brockett, an undergraduate student, is an author on this manuscript for research he did in the classroom! My passion for understanding how an organism develops from a single cell drives my research, and the feeling I get when I see my mentees succeed while studying these mechanisms provides the fuel that keeps me going.
How has your research been affected by the COVID-19 pandemic?
BC: For me, COVID-19 hit right as I was finishing the experiments for two of my postdoctoral projects. During the ∼2-3 month lab shut down I was able to stay productive by submitting and revising manuscripts, but being away from the lab made it hard to advance interesting new ideas. The thing I miss most about not being able to go into lab is my ability to bounce crazy ideas off my talented Katz lab colleagues.
Before your work, what was known about the role of inherited histone methylation in the germline/soma distinction?
BC, DK: This paper is really about two major lines of research coming together to create a new story. We had been working on how two histone modifying enzymes, the H3K4me1/2 demethylase LSD1 (SPR-5 in C. elegans) and the H3K9 methyltransferase MET-2 cooperate to reprogramme histone methylation at fertilization to prevent the inappropriate chromatin environment from being passed on from one generation to the next. We had found that a failure to reprogramme histone methylation in spr-5; met-2 double mutants causes a maternal effect developmental delay and sterility phenotype. We were interested in how the inappropriate inheritance of histone methylation causes the developmental delay. Dr Susan Strome, with some help from Dr Bill Kelly, had performed some beautiful work showing how maternal deposition of the H3K6 methyltransferase is required transgenerationally to help specify the germline in progeny. Brandon had noticed some similarities between the developmental delay that we were observing and some high temperature phenotypes that Susan Strome had shown and were continuing to be worked on by Dr Lisa Patrella in her own lab. As detailed below, Brandon was able to show that the MES-4 system and the SPR-5; MET-2 reprogramming mechanism antagonize one another. It is also important to note that several labs have identified somatic repression mechanisms that antagonize the MES-4 system. We are interested in seeing how these systems interface with SPR-5; MET-2 reprogramming, so stay tuned!
Can you give us the key results of the paper in a paragraph?
BC, DK: We had previously shown that SPR-5 and MET-2 act together to repress germline genes at fertilization. In this paper, we found that H3K36 methylation antagonizes this repression to prevent these germline genes from being completely shut down. Without inherited H3K36 methylation, the germline is not properly specified. In contrast, without SPR-5; MET-2 repression, H3K36 is inappropriately propagated to the soma, resulting in germline genes being inappropriately expressed there. The inappropriate expression of germline genes in the soma results in a developmental delay. Thus, neither SPR-5; MET-2 reprogramming nor the MES-4 germline inheritance system can properly function without each other. Instead SPR-5, MET-2 and MES-4 coordinately balance three difference histone modifications (H3K4, H3K9 and H3K36 methylation) to ensure that germline versus soma is properly specified.
Single molecule fluorescence in situ hybridization image of a C. elegans L1 larvae ectopically expressing a germline-specific gene, htp-1, in somatic tissues (grey, htp-1mRNA; blue; DAPI).
Why do you think inappropriate somatic expression of germline genes causes developmental delay?
BC, DK: As discussed in the paper, we think that there are two possible mechanisms for how the ectopic expression of germline genes causes developmental delay in spr-5; met-2 mutants. One possibility is that transcription of the germline programme itself causes the developmental delay. For example, if germline transcription factors are competing with somatic transcription factors to turn on genes, it is possible that the mix of proteins generated is simply too confusing for the cell to commit to its proper cell fate. The alternative is that a part of the germline function interferes with somatic development; for example, the germline precursors undergo a cell cycle arrest. It is possible that the proteins involved in this germline cell cycle checkpoint slow the progression of somatic cells via cell cycle regulation. Consistent with this latter possibility, we show that spr-5; met-2 mutants can silence an extrachromosomal array in the soma. This function, which is normally confined to the germline, suggests that somatic tissues in spr-5; met-2 mutants make proteins that can perform some germline functions. Thus, it is possible that a germline function acting in the soma prevents somatic cells from quickly adopting their proper cell fate.
What relevance do your data have for human patients harbouring mutations in histone-modifying enzymes?
BC, DK: Recent genome sequencing has revealed that several neurodevelopmental disorders are caused by mutations in histone-modifying enzymes. These include mutations in: (1) the H3K36 methyltransferase Setd2, the H3K27 demethylase Kdm6a and the H3K4 methyltransferase Kmt2d, which cause Kabuki Syndrome; (2) the human orthologue of spr-5, LSD1, which causes a Kabuki-like Syndrome; and (3) the H3K36 methyltransferase Nsd1, which causes Sotos Syndrome. Similar to what we observed in spr-5; met-2 mutant progeny, many of the human patients with mutations in these histone-modifying enzymes suffer from global developmental delay. Based on our model, it is possible that the developmental delay in these patients may be caused by the failure to properly regulate histone methylation during essential developmental transitions. Consistent with this, we have recapitulated some phenotypes in a maternal hypomorphic mutant of Lsd1 in mice that are reminiscent of Kabuki Syndrome. We hope that by continuing to study how mutations in histone-modifying enzymes in C. elegans and mice give rise to developmental defects, we will shed light on the human diseases caused by defects in histone-modifying enzymes.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
BC: As detailed above, I had made the observation that the developmental delay we were observing had some similarities to some high-temperature phenotypes that Susan Strome had shown and were continuing to be worked on by Lisa Patrella in her own lab. This raised the possibility of a connection between SPR-5; MET-2 reprogramming and the MES-4 inheritance system. The crucial test of this potential connection was to knock down mes-4 via RNAi and see if it rescued the developmental delay, and we were very excited to find that it did rescue it, and even more excited when our RNA-seq subsequently showed that MES-4 germline genes are expressed in the somatic tissues of spr-5; met-2 mutants. After this independent confirmation of the connection between the two systems, we were confident that we had figured it out.
And what about the flipside: any moments of frustration or despair?
BC: The most frustrating part of this project was trying to gather enough L1 larvae to perform the initial genomic experiments. When we first started the project, there were no strains available that could balance the spr-5 mutant allele. I had to genotype every single hermaphrodite parent! At one point, I thought I would never get enough larvae to perform the genomic experiments. But David saw on science Twitter that the Caenorhabditis Genetics Center (CGC), which houses C. elegans strains, was developing new balancer strains. I contacted them and was able to get the FX30208 tmC27 [unc-75(tmls1239)](I) balancer even before they made it available to the broader C. elegans community. By reporting back that it worked well, I was also able to give back to the C. elegans community.
What next for you after this paper?
BC: I am officially on the academic job market searching for a tenure-track position and developing exciting new projects of my own that stem from this paper. We have mounting evidence that mutations in highly conserved histone-modifying enzymes may give rise to developmental phenotypes in vertebrates that are similar to what we observe in C. elegans. I want to take advantage of C. elegans mutants that fail to properly inherit histone methylation to further investigate how inherited chromatin states affect complex developmental processes like cell-to-cell communication and cell migration. I am also interested in potentially introducing the human version of Lsd1 into C. elegans to humanize the worm so that I can generate mutations that have been found in the human LSD1 patients. This type of approach is on-going through the NIH-funded Undiagnosed Diseases Network (UDN).
Where will this story take the Katz lab?
DK: We believe that spr-5; met-2 double mutants provide an excellent model for understanding how cells respond to inappropriately inherited histone methylation. We are taking advantage of the invariant embryonic cell lineage in C. elegans by performing automated lineage tracing experiments in spr-5; met-2 mutants. This will enable us to understand cell by cell how inappropriately inherited histone methylation affects processes such as cell division timing, cell migration, programmed cell death, etc. We hope to combine this with single cell RNA-seq to ask how each cell responds transcriptionally to this inappropriately inherited histone methylation. So stay tuned.
Remarkably, trying to understand the regulation of histone methylation in the germline has also taken us into the Alzheimer’s disease field. While trying to understand whether SPR-5; MET-2 reprogramming is conserved in mice, we serendipitously discovered that LSD1 is continually required for the survival of hippocampus and cortex neurons. We are interested in the possibility that terminally differentiated cells continually employ histone-modifying enzymes, such as LSD1, to maintain their cell fate. In the meantime, we have gone on to provide evidence that LSD1 is inhibited by pathological aggregates of tau in mice and human Alzheimer’s disease patients. We believe that this inhibition is a crucial part of how pathological tau induces neurodegeneration. So, you never know where developmental biology will lead!
You never know where developmental biology will lead!
Finally, let’s move outside the lab – what do you like to do in your spare time in Atlanta?
BC: I like to go hiking with my 5-year-old twin daughters, play golf, and find cool breweries who push the edge on brewing delicious stouts and IPAs!
DK: I enjoy soccer with my 13-year-old twins and co-host a popular Atlanta United podcast. I also co-founded a very small vineyard just outside Atlanta at a friend’s house, and we have just produced our first successful vintage of a Norton/Cabernet Sauvignon blend. But I am also happy to drink a local beer with my outstanding postdoc Brandon.
(No Ratings Yet)
Loading...
