The people behind the papers – Ramya Ranganathan and Andrea Streit

Ramya Ranganathan (left) and Andrea Streit (right).

Andrea, what questions are your lab trying to answer?

AS: We study early development of the sensory nervous system in the head – the ear, the eye, olfactory epithelium and cranial ganglia. Although they are very different in adults, they share common progenitors and develop from patches of epithelia called placodes. We are particularly interested in the transcriptional networks that control how placode progenitors diverge from the central nervous system and neural crest precursors, and how placodal cells become different from each other. We are very excited about our single-cell data showing that an individual progenitor initially co-expresses large gene modules that later characterise definitive cell types and are now using our enhancer data to figure out how this is resolved.

Ramya, how did you come to work in the lab and what drives your research today?

RR: After my Master's in Neurosciences, I worked briefly as a junior research fellow in India when I got interested in cell fate decisions. When I moved to London, I initially joined Andrea's lab as a research assistant because I was excited about her group's research focus on how common sensory precursors give rise to a broad range of sensory cells. While working on this project, I realised that although Six1 is one of the master regulators for sensory placode development, very little was understood about its downstream targets. I wanted to have a go at solving a part of this black box. This is how my journey began as a researcher. I love solving problems and the fact that you get to explain a part of nature's mystery excites me the most. I am still fascinated by how cell fate decisions are made during development with such high precision.

Andrea, can you tell us about the background of the field that inspired your work?

AS: There are two aspects to this – our interest in developmental mechanisms and in human disease. The transcription factor Six1 and its co-factor, Eya1, have long been implicated in different aspects of sense organ development. However, how they act and the molecular pathways downstream of these factors were completely unknown. Characterising the regulatory regions in ear progenitors was an ideal opportunity to explore this. Secondly, in humans, mutations in these genes cause branchio-oto-renal syndrome, even though about half of the individuals presenting with the disease phenotype have no mutations in these genes. We reasoned that discovering Six1 targets might point to new candidate disease genes.

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

AS & RR: The main aim of this paper was to identify Six1 downstream targets in inner ear precursors. First, we scanned our previously identified ear-specific enhancers for Six1 motifs and then used our transcriptomic data to link these to genes expressed in ear progenitors. Selecting a few genes for further investigation, we then showed that Six1 motifs are required for normal enhancer activity. Further, Six1 binds to these enhancers and regulates the associated genes in both chick and frog. Finally, using RNA sequencing from human otic vesicles, we confirmed that many of the targets identified in chick are also expressed in humans. Moreover, about a quarter of our targets are located in known human deafness loci, where the causative gene has not been identified. This is very exciting as it prioritises these newly identified targets as candidate deafness genes.

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

RR: The moment that stuck with me the most was when I started to see the enhancer activity reporter assay light up green only in the otic placode or have an expression pattern similar to the gene it is associated with. Seeing the abstract concept of gene regulation by cis-regulatory elements live in action in a growing chick embryo was fascinating and is still a memory. I remind myself of that moment when I have disappointing phases in my research.

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

RR: This was a very challenging project due to redundancies in Six1 function by other members of the Six family: the traditional knocking down/knockout approach was not going to work. This meant a lot of frustration that pushed us to think out of the box. When I started the project, the chicken genome was not robust, but, thankfully, there has been much progress on that front in recent years. With very few cells to work with and the genome not being well characterised, we needed a lot of patience and troubleshooting to do this work. The only positive is that the entire team gets closer due to long brainstorming sessions, which was always fun.

Why did you choose to submit this paper to Development?

AS & RR: Development remains one of the leading journals in developmental biology run by scientists for scientists. We felt that linking the developmental mechanisms of early ear development to human disease would be of interest to the community.

Andrea, what is next for you after this paper?

AS: I have started as a research fellow at University College London, UK, in Vilaiwan Fernandes’ lab. I am currently working on a project trying to dissect the molecular mechanisms underpinning the onset of neuronal differentiation using the Drosophila visual system as a tractable model. So, my quest to understand mechanisms involved in the precise regulation of cell fate decisions and dissecting the gene regulatory networks during development continues.

Andrea, where will this story take your lab next?

AS: Having characterised the gene network controlling early inner ear development, we have exciting stories coming up that look at how these networks changed during evolution. Of course, we are also keen to explore whether the genes we have identified are indeed related to deafness, which will require functional analysis and working with human geneticists.

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

AS: I love going on long country walks with my dog and travelling the world to explore different cultures and diverse food. While doing this, I am always on the look-out for unusual things to photograph.

RR: I love to listen to music, practise my dance skills and spend time with family. I have a 5-year-old son – I enjoy doing artwork with him and he inspires me to stay curious.