The nuclear pore has been thought to have a consistent function during development, although its composition can vary. In this issue, Valentyna Kostiuk and colleagues reveal a context-specific role of a nucleoporin, Nup107, in the maternal-to-zygotic transition. We caught up with first author Valentyna Kostiuk and corresponding author Mustafa Khokha, Professor and Principal Investigator at Yale School of Medicine, USA, to learn more.
Valentyna Kostiuk (left) and Mustafa Khokha (right)
Mustafa, what questions is your lab trying to answer?
MK: We are interested in the molecular basis of congenital anomalies. Congenital anomalies are alterations in normal embryonic development. As a physician-scientist, I care for children that present to the Pediatric Intensive Care Unit and many of them have congenital anomalies. We perform trio-based sequencing of these children to identify candidate genes that may explain their disease. In most cases, the candidate genes that we identify have no established role in embryonic development, and, therefore, we employ Xenopus, a frog model, to study the molecular mechanism of the candidate gene in development. Frogs are an ideal model for human development given their balance between experimental speed and efficiency and evolutionary conservation. Finally, by establishing a molecular mechanism, we begin the journey to understand the disease process, which can have an important impact on our patients.
Valentyna, how did you come to work in the lab and what drives your research today?
VK: My interest in Dr Khokha's work stemmed from two key aspects: the patient-driven approach and the wide variety of biological topics explored in the lab. I found it deeply inspiring to select a research project based on a patient's phenotype. It was incredibly meaningful to study a topic rooted in the unique presentation of an individual with a specific malformation, rather than focusing on a predefined pathway. This approach not only added a personal dimension to the research but also presented a stimulating intellectual challenge. Working on phenotype-driven research often led me to unexpected biological processes, such as microRNA processing. With no prior experience in this area, I had to acquire new skills by collaborating with experts in the field. The novelty of this work, coupled with the collaborative opportunities it provided, was both rewarding and inspiring. These experiences continue to fuel my curiosity and drive my passion for further exploration in this field.
These experiences continue to fuel my curiosity and drive my passion for further exploration in this field
Can you tell us about the background of the field that inspired your work?
MK & VK: This project explored the role of nucleoporin 107 (Nup107) in congenital heart disease, a leading cause of mortality in the paediatric population. Despite the identification of multiple candidate genes in children with cardiac malformations, the molecular mechanisms underlying these malformations remain largely unknown. The primary goal of this study was to uncover how mutations in Nup107 could lead to such developmental defects. I chose to focus on Nup107 because it is a key component of the nuclear pore complex, an essential cellular structure that regulates nucleocytoplasmic transport. Given its fundamental role in cellular biology, it is particularly intriguing that mutations in Nup107 could result in organ-specific defects such as congenital heart disease. Understanding these mechanisms has the potential to not only elucidate the pathogenesis of congenital heart disease but also inform future therapeutic approaches for this significant clinical challenge.
Can you give us the key results of the paper in a paragraph?
MK & VK: At first, we thought that depleting Nup107 would simply halt development or lead to embryonic death, as nuclear pores are essential for all nuclear-cytoplasmic traffic. But, we identified a NUP107 variant in a patient and we had found previously that mutations in other nucleoporins could cause tissue-specific, developmental defects. We demonstrated that Nup107 plays a crucial role in early embryonic patterning and subsequent organ development. Specifically, the loss of Nup107 directly impacted germ layer specification, left-right patterning and cardiac looping, leading to altered heart structure. These developmental disruptions were linked to the role of Nup107 in regulating a key step during the maternal-zygotic transition. In particular, Nup107 enhances the nuclear retention of the pri-miR427 transcript, enabling it to be processed by Drosha to facilitate the clearance of maternal transcripts. In Nup107-depleted embryos, however, the pri-miR427 transcript failed to remain in the nucleus and was instead mislocalized to the cytoplasm, where it could not undergo processing by Drosha. This mislocalization resulted in reduced production of mature miR427, which, in turn, impaired the degradation of maternal transcripts, resulting in altered embryonic development.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
VK: One of the most fascinating moments in this research process occurred when I performed an in situ hybridization to detect the tissue localization of pri-miR427. In Nup107-depleted embryos, I observed a striking lack of nuclear localization for this transcript – something I had never encountered in any of my previous in situ hybridization experiments. The specificity of this localization was so compelling that we decided to confirm the finding using an alternative method, RNAScope, which yielded consistent results. While prior studies had demonstrated that Nup107 depletion can affect mRNA localization, its potential role in pri-miRNA localization was previously unknown, making this discovery particularly exciting and groundbreaking.
And what about the flipside: any moments of frustration or despair?
VK: A challenging moment in my research came when we analysed the RNA-sequencing results from our 12-h time-course experiment. As anticipated, the experiment produced a substantial amount of data, and I was hopeful that it would steer my project toward understanding germ layer differentiation – the primary phenotype I had observed in the context of Nup107 depletion. However, an unexpected discovery emerged: the common link among these transcripts was that they were predominantly maternal transcripts. This surprising finding shifted the focus of our investigation. We began exploring the mechanisms by which these maternal transcripts are cleared, ultimately leading us to initiate experiments evaluating miR427.
Why did you choose to submit this paper to Development?
MK & VK: We chose to submit our paper to Development because our findings reveal multiple crucial insights into the maternal-zygotic transition, which we believe will be of interest for the journal's broad audience of cell and developmental biologists. Through our investigation of individual steps of the maternal-zygotic transition, we demonstrated that transcription at the miR427 locus remains unaffected. However, the loss of Nup107 results in the premature export of pri-miR427 from the nucleus, preventing its nuclear processing by Drosha. This disruption significantly diminishes the production of mature miRNA, impairing downstream processes. Our study integrates several key discoveries: (1) the temporal role of Nup107 during the blastula stage; (2) its specific function in nucleocytoplasmic exchange and impact on miRNA processing; and (3) the resulting persistence of maternal transcripts and the downstream effects on germ layer specification. These interconnected findings provide valuable insights into the complex regulation of early embryonic development.
What is next for you after this paper?
VK: Currently, I am investigating the role of another candidate gene in left-right patterning and examining how mutations in this gene influence the Nodal pathway. This project marks my first foray into Nodal signalling since joining the lab 5 years ago. The connection between this new research focus and the malformations observed in the patient cohort underscores the unique and exploratory nature of patient-centred research. I am excited to delve into this topic and uncover insights that bridge clinical observations with fundamental biological mechanisms.
Where will this story take your lab next?
MK: There are many patients for whom we have identified interesting candidate genes. So, we are always screening new candidate genes and chasing after molecular mechanisms. The exciting part is that I really have no idea where it will take us next. If you had asked me at the start whether Nup107 is a gene that regulates development I would have said probably not. It is a protein essential for the basic functions of any cell – nuclear-cytoplasmic communication. But having found a patient with congenital heart disease and a variant in NUP107 made us rethink that possibility. That led Valentyna to an exciting and unexpected scientific journey.
Finally, let's move outside the lab – what do you like to do in your spare time?
VK: I enjoy spending time outdoors and staying active, as it allows me to recharge and connect with nature. One of my favourite activities is hiking, when I can immerse myself in the beauty of the trails and discover new landscapes. I also love exploring the picturesque bicycle trails scattered across New England, which offer both a physical challenge and a chance to appreciate the region's natural charm. Beyond outdoor adventures, I have a passion for music and cooking. I play the piano, which provides me with a creative outlet and a way to unwind after a busy day. In the kitchen, I enjoy experimenting with new vegetarian recipes, blending flavours and techniques to create delicious and wholesome meals. These hobbies keep me balanced and energized for my professional endeavours.
Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
E-mail: [email protected]