Transitions in development – an interview with Momoko Ikeuchi

Let's start from the beginning – when did you first become interested in science?

When I was a kid, I already wanted to become a scientist. I was influenced by my family, because my father is a scientist who works on photobiology using cyanobacteria. He would share his excitement of science with us. I remember one day he brought home a gel image. I didn't know what it was, but I just remember how excited my father was. My mother would tell me that he could make money by just doing what he wanted to do. It sounded like a dream job!

Have you always been interested in plants?

Plants have always fascinated me; the way that plants live is very interesting. Plants appear to be passive and weaker than animals, but they flourish on Earth. I was simply curious about their survival strategies. I also love seeking out various plants in nature by going into the mountains. I especially love the weird-shaped leaves of ferns. There are hundreds of species of ferns in Japan because the weather here is quite humid. That was how I became interested in the morphological diversity of plant organs.

You did your PhD at the University of Tokyo – what did your research focus on?

For my PhD, I chose a lab that studied leaf development. My first project was about a regulator of leaf shape in Arabidopsis. Initially, I expected it to work as a mobile signal to regulate organ morphology. But, as the project went on, I found out that it was not actually secreted, so I wanted to shift to a different project. Because of my interest in morphological diversity, I chose to work on the California poppy (Eschscholzia californica) and some related species. Even though the project was interesting, it was technically too challenging. By the end of my PhD, I was almost ready to give up academia, because none of my projects worked out as I originally anticipated.

Despite the setbacks during your PhD, you managed to find a postdoctoral position at RIKEN. Could you tell us more about your time there?

Becoming a scientist was my childhood dream, so I just wanted to give it one last try. During my graduate study, I became more interested in plant development at the cellular level. The timing of cellular differentiation has an important impact on morphogenetic events. That's the main reason why I chose Keiko Sugimoto's lab for my postdoctoral research.

The Sugimoto lab originally focused on the processes of cellular differentiation in a normal developmental programme. Another researcher at the lab, Dr Akira Iwase, found an important regulator of cellular de-differentiation that plays a crucial role in callus formation and organ regeneration. They were recruiting a postdoc to work with him. I joined the lab at a very exciting moment. I expected that studying cellular de-differentiation would give us new ideas on the cellular differentiation. Indeed, we successfully found a regulatory mechanism on cellular differentiation from our study on cellular de-differentiation. In the study (Ikeuchi et al., 2015), we initially found an intriguing phenotype of Polycomb Repressive Complex 2 (PRC2) mutants, where the highly differentiated cells spontaneously de-differentiate to become callus and embryos in planta. This was a surprising finding, as it means that the histone methyltransferase PRC2 plays a role in maintaining a differentiated status of mature somatic cells! During my postdoc period, I fortunately worked on several amazing projects, including this one, and I gradually became more confident in pursuing an academic career.

You started your own group at Niigata University in 2019, and then relocated your lab to Nara Institute of Science and Technology (NAIST) in 2022. How was your experience looking for a PI position?

The process of finding a PI position took me more than 2 years. I started searching for a PI position in 2017, which was 5 years after getting my PhD. I was strongly influenced by my lab mates from Europe, where it is pretty common to become PI at that career stage, whereas in Japan people usually become a PI much later, often more than 10 years after their PhDs. I was considered too junior to find a PI position in Japan at that time. I was interviewed six times in different European institutions, but I didn't get any offers. In the end, I accepted an offer from Niigata University in 2019. I was the youngest Associate Professor in the department.

At Niigata University, teaching and administrative duties were pretty heavy. As a junior PI, I wanted to put more of my effort into doing research. That was the main reason why I decided to relocate to NAIST. NAIST is a research-oriented institute with no undergraduate courses, so there is much less teaching compared with other universities.

Can you summarise the research themes of your group? How did you navigate the field to find your niche?

The field of organ regeneration in plants is rapidly growing. More people are interested in the regulatory mechanisms of regeneration, but, in my opinion, the basic developmental framework of organ regeneration is still not well understood. So, I decided to focus my research on the developmental mechanisms of organ regeneration and, specifically, how calluses make new shoot apical meristems.

Callus has a heterogeneous cell population with many different cell types, but plants are able to establish newly ordered apical meristem from callus. I want to understand how plant cells manage to do that. Meristem initiation is very unpredictable, making it difficult to follow its development. That is why our understanding of meristem initiation from calluses is limited. In the lab, we use single-cell RNA sequencing to characterise the cell types in callus and perform live imaging to see the developmental trajectory of meristem initiation.

Another direction I would like to pursue in my lab is other plant model systems, as I am interested in the diversity in nature. When we wrote a Review article for Development in 2016 (Ikeuchi et al., 2016), we did a lot of literature searching about the diversity of regeneration events. I realised that what we learn from Arabidopsis is just one typical mode of regeneration, but there are other modes of organ regeneration in plants. That is why I want to figure out the developmental mechanisms of the different modes of organ regeneration.

What are the current exciting areas in plant regeneration?

Single-cell RNA sequencing analyses give us a great opportunity to understand the still mysterious cellular mechanisms underlying organ regeneration. We have a recent publication (Ogura et al., 2023) where we found an important regulator of cell fate specification of callus. In the future, I hope we can figure out individual physiological roles of the specific cell types in the calluses. In general, understanding organ regeneration at a cellular level would greatly improve our understanding of the development mechanisms, but we can also use that information in the agricultural and horticultural field to improve the efficiency of tissue culture in crops. I think it has a great potential for plant research in the future.

How did you find the transition to group leader? What were the best moments? What were the most challenging moments?

I really enjoy being a PI – I feel like I'm doing a better job compared to when I was a postdoc! I love the team-building aspect of running a lab. The best feeling as a PI is when my team of students, postdocs and collaborators can go much further than I could as an individual.

As for challenging moments, I find managing the different responsibilities difficult. When I was at Niigata, I didn't have much time to work on my manuscripts or discuss science with my students. As a PI, I have more responsibilities, and I have to be able to multitask well.

How do you approach hiring new team members?

If you are a new PI, I guess it is generally not so easy to recruit people, because postdocs and students often choose bigger, more prestigious labs. In my case, I personally contact potential candidates I know. In Japan, we have these strategic group grants consisting of multiple labs in the same research area across Japan, which is a good opportunity to make contacts and identify potential students and postdocs. A new postdoc started this April, whom I got to know in a meeting of that strategic group. I believe that being proactive and contacting potential candidates helps, rather than just waiting for the applications to come in.

What advice would you give to people just starting their own labs?

Having a good support network is truly important. After becoming independent, I sometimes felt lonely, and a huge sense of responsibility. Networking with my friends in the field and other disciplines helped me a lot. Having close friends going through similar situations and sharing struggles or concerns is very helpful mentally and physically.

How about support from mentors? Were there any mentors who helped you as you transitioned to group leader?

My postdoc supervisor, Keiko, is a great mentor to me. Keiko encourages postdocs and students a lot and creates a very collaborative environment in the lab. She is an amazing role model as a PI, and she greatly supported me during my search for a group leader position.

You have done several interviews in the media about your research. What is your view on the importance of communicating your science to non-scientists?

Communicating with non-scientists or scientists from different disciplines means a lot to me. These opportunities help me to place my specific scientific interests in a broader context. In my opinion, as scientists we have a responsibility to share the excitement of new findings with a broader audience, and I personally enjoy these opportunities so much.

Did you ever consider an alternative/non-academic career path?

When I was a small kid, I loved reading and wanted to be a novelist. Now, I enjoy writing manuscripts and grant proposals, but writing popular science books is still on my bucket list!

What do you like to do outside of the lab?

I love hiking and looking for alpine plants and ferns. I especially like Yakushima in the southern part of Japan. Yakushima is a semi-tropical island with interesting biological diversity of the plants and animals. In my daily life, I enjoy visiting temples and other historical places as well, as our institute is close to a historical city called Nara, where the ancient government was located.

Finally, is there anything else you want to tell Development readers?

I want to mention a Development paper (Gookin and Assmann, 2021) that cited my first ever publication (Ikeuchi et al., 2011) during my PhD, to illustrate a point about the value of publishing findings even if there isn't a nice, complete story. During my PhD, I observed this weird structure in a mutant I was working on, which had no name. Somehow, the authors of this 2021 paper cited my publication! I was surprised and also very happy because this is the beauty of the continuity of academic publishing. When we write our manuscripts, we always want to make an excellent story, but sometimes it doesn't work out. If we publish the data anyway, someone else may be able to build on that data to produce new findings – that is how science can progress.

Momoko Ikeuchi was interviewed by Joyce Yu, Online Editor at Development. This piece has been edited and condensed with approval from the interviewee.