using a lightsheet microscope for ~188 hours.
Akanksha Jain is the new Assistant Professor for Neural MorphoGenomics (tenure track) at the University of Zurich. This professorship was set up with a generous donation to ZNZ and support from the URPP “Adaptive Brain Circuits in Development and Learning”. In our interview, she discusses how her research explores the dynamic processes that shape human brain during development, the interdisciplinary approaches behind her work, and her vision for building a collaborative research environment in Zurich.
Hi Akanksha, welcome to the ZNZ community ! You’ve just taken up your new role as Assistant Professor at the University of Zurich. Your research focuses on how the human brain takes shape during development and how these processes are disrupted in disease. What are the key questions driving your work, and why do you think they are important to address?
At the core of my research is the question: How does the human brain build its architecture? I study how mechanical and molecular processes interact to shape cell behavior and tissue organization, and how small disruptions early in life can have long-lasting effects.
This is important because many neurological and psychiatric disorders arise from subtle developmental changes rather than single gene defects. By combining live imaging with single-cell and spatial molecular approaches, my lab aims to uncover shared mechanisms of brain development and disease and identify stages where early intervention may be possible.
Your research brings together stem-cell–derived brain organoids, long-term imaging, and single-cell genomics. What does this combination allow you to see or understand about brain development that would remain hidden with more traditional approaches?
Bringing stem-cell–derived brain organoids together with long-term live imaging and single-cell genomics allows us to move beyond static descriptions of brain development and instead capture development as a dynamic, quantitative process. Brain organoids provide access to human-specific early neurodevelopmental programs in an experimentally tractable system, while long-term imaging lets us follow individual cells and tissue trajectories over time, tracking proliferation, migration, morphogenesis, and interactions as they unfold. Single-cell and spatial genomics then allow us to connect these observed behaviors to underlying molecular and regulatory states.
What makes this particularly powerful is that it creates a foundation for quantitative, mechanistic screening assays. By integrating imaging, genomics, and computational analysis, we are developing interdisciplinary pipelines that can systematically measure how genetic perturbations, environmental factors, or candidate compounds alter developmental trajectories. This opens the door to scalable drug discovery and phenotypic screening in a human-relevant brain development context.
Beyond discovery, this framework is also relevant for regenerative and stem cell–based therapies. Understanding how neural cells emerge, mature, migrate, or fail provides essential insights for improving cell replacement strategies and guiding tissue engineering approaches. In short, this combination allows us not only to observe development in unprecedented detail, but also to turn brain development into a quantifiable, testable, and therapeutically actionable system – something that remains largely inaccessible with more traditional models.
Many neurological and psychiatric conditions are thought to have their origins early in life. How can studying developmental processes in organoids help bridge the gap between early brain development and disorders that emerge much later?
Many brain disorders manifest clinically years or even decades after birth, but their origins often lie in early developmental events. We are developing quantitative assays to track cell type emergence and migration during brain regionalization and maturation. Many specific cell types are implicated in neurodevelopmental or psychiatric brain disorders, but understanding how certain mutations affect developmental programs – such as the emergence and migration of these cells – has remained challenging, especially for the human brain.
Organoids model several of these early neurodevelopmental stages and generate a wide variety of brain region–specific cell types, providing a way to reconstruct those early trajectories in a controlled and human cell–derived tissue system. By introducing disease-relevant genetic variants, patient-derived cell lines, or environmental perturbations and tracking their effects over developmental time, we can identify early cellular or tissue-level deviations that may later amplify into dysfunction. Importantly, this approach allows us to distinguish primary developmental defects from secondary or compensatory changes, which is very hard to do in patient samples alone. In this way, organoids act as a bridge between genetics, development, and disease progression, helping us understand not just what goes wrong, but when and how it starts.
Starting an independent research group marks an exciting transition. What are you most looking forward to in this new phase – both scientifically and personally – and what kind of research environment do you hope to build in Zurich over the coming years?
Scientifically, I’m most excited about the freedom to pursue bold, challenging questions, to interact with a new scientific community that will shape my ideas and knowledge, and to develop technologies that didn’t exist when I was a trainee. I’m particularly looking forward to building long-term, collaborative projects that connect neurodevelopmental biology, imaging, genomics, and biophysical theory. Beyond understanding the fundamental aspects of human brain development, I feel this is imperative in realizing the vision of making organoid models reliable resources for understanding disease mechanisms and aiding drug discovery.
Personally, starting my own group is a very exciting time! It is an opportunity to expand my research horizons, build a team, and work together to shape a research culture. I hope to build an environment that is curious, creative, supportive, and intellectually generous, where people feel encouraged to take risks, ask fundamental questions, and learn across disciplines. I am thrilled to start this journey in Zurich, as the scientific landscape in this city offers an ideal environment to pursue challenging questions, especially in the field of human neurodevelopment. Zurich is an ideal place for this: it has strong basic science, excellent infrastructure, and a collaborative spirit that makes it easy to connect across fields.
Finally, for early-career researchers who are interested in interdisciplinary neuroscience but may feel unsure about how to navigate such a path, what advice would you give based on your own experience?
Interdisciplinary work offers challenges but is also very exciting and rewarding, with lots of scope for new ideas and approaches to the same questions. My main advice is to take the challenges head on, read a lot, and train yourself to think from multiple perspectives to come up with creative solutions. If you feel stuck, there is a huge scientific community around us that is ready to help, so reach out as much as you can.
Interdisciplinary work often means feeling like a beginner more than once, and that’s not a weakness – it’s part of the process. It’s important to build strong expertise in something, so you have a solid foundation, but also to actively seek out collaborators and mentors who think differently from you. I firmly believe that one has to remain curious, ask naïve questions, interact with peers and mentors, and invest time in learning the language of other fields. Finally, one has to be patient with oneself. Interdisciplinary paths can look less linear, but they often lead to the most creative and impactful science.
Thank you for sharing your perspective, and we wish you all the best as you embark on this new chapter at UZH.
Useful links:
Images:
Akanksha Jain, Department of Molecular Life Sciences, University of Zurich