A large international consortium has created the first complete atlas of all the cells of the fruit fly, a small but mighty creature. Scientists from the Champalimaud Foundation participated in the massive effort.
Fruit flies have played a leading role in biological research for over a century, ever since Thomas Hunt Morgan used these tiny insects to discover that genes reside on chromosomes, essentially uncovering the mechanical basis of heredity. Many scientists followed in Morgan’s footsteps and several went on to win a Nobel Prize for their groundbreaking discoveries using this small model organism.
Despite their size, fruit flies are more similar to humans than their appearance may suggest. Of the approx. 14,000 protein-encoding genes in the fly genome, about two-thirds have a human counterpart. Aside from key insights into the basic workings of biological mechanisms such as genetics and developmental biology, fruit flies have played a vital role in developing treatments for cancer, immune disease and diabetes, to name just a few.
The single-cell revolution
With the advent of single-cell genomic technology, scientists have been able to study tissues at unprecedented resolution, looking at the expression of all genes simultaneously in thousands of individual cells. Such fine-grained insights can help to decipher how certain cells differ from and interact with their neighbours, and how they form and function in the tissue.
With the fruit fly as popular as ever in biomedical research – small in size, easy to breed – single-cell analysis has quickly gained traction in this research community.
“Several research groups across the globe, including my own, have recently applied single-cell sequencing to different fruit fly tissues at different developmental stages,” says Stein Aerts, group leader at VIB and KU Leuven in Belgium. “The problem is that these data have been generated by different laboratories on different genetic backgrounds with different protocols and sequencing platforms, which has hindered the systematic comparison of gene expression across cells and tissues.”
Stein Aerts is one of the founders of the Fly Cell Atlas consortium, which grew organically after gathering specialists in the fly research community to Leuven back in Dec 2017. What began as wild plans forged over Belgian beers has now become a reality: after four years, many meetings, and a lot of hard work, the consortium now presents the first complete Fly Cell Atlas in Science.
Teamwork makes the dream work
“This was really a titanic piece of work,” says Liqun Luo of Stanford University, who co-lead the endeavour together with Aerts, and three other leading figures in the field: Stephen Quake, at Stanford and the Chan Zuckerberg Biohub (CZ Biohub); Bart Deplancke at EPFL; and Norbert Perrimon at Harvard. “The entire consortium involved 158 experts from 40 different laboratories across the world and was supported both technically and financially by the CZ Biohub.”
Two early-career researchers on opposite sides of the Atlantic spearheaded the data generation and analyses: Jasper Janssens, a soon-to-graduate PhD student at VIB-KU Leuven, and Hongjie Li, an Assistant Professor at Baylor College of Medicine and previously a postdoc in Luo’s lab at Stanford.
On the Champalimaud Foundation side, the co-authors of the article now published in Science are Carlos Ribeiro, principal investigator of the Behaviour and Metabolism laboratory; Zita Santos, Darshan Dhakan and Ibrahim Tastekin, postdoctoral researchers, and Rita Figueiredo, PhD student – all members of Ribeiro’s laboratory.
Hongjie Li says: “We aimed to establish a cell atlas for the entire adult fruit fly — with the same genetic background, dissociation protocol and sequencing platform. In this way, we’d be able to obtain a comprehensive categorisation of cell types, integrating our single-cell transcriptome data with existing knowledge about gene expression and cell types, to systematically compare gene expression across the entire organism and between males and females. It would also allow us to identify cell type-specific markers across the entire organism.”
The team took two complementary strategies to achieve their goal, adds Jasper Janssens: “We sequenced single cells from dissected tissues so we knew the identity of the tissue source, but we also sequenced cells from the entire head and body to ensure that all cells were sampled.”
After sequencing all the fly cells, it was necessary to make sense of the enormous amount of data generated. A task impossible to be carried out by a single work team. To overcome this challenge, a consortium of specialists capable of identifying and annotating the different types of cells was created. This was one of the important contributions of Carlos Ribeiro’s laboratory at the Champalimaud Foundation, in particular in the annotation of data from brain cells, ovaries and adipose tissue of the fly.
The resulting dataset, named Tabula Drosophilae – for Drosophila melanogaster, the Latin name of the fruit fly – contains more than 580,000 cells, resulting in >250 distinct cell types.
“Many of these cell types are characterised for the first time, either because they emerged only after increasing cell coverage or because many of them can only be profiled using single-nucleus RNA sequencing, which is another technical highlight of our study,” adds Jasper Janssens.
This work allows us, for the first time, to compare the transcriptome, i.e. the map of active genes, between different cells within the same organism and question what makes them similar or different. Cell metabolism has recently gained a lot of attention as it is known to be altered in various diseases such as cancer or diabetes. However, to understand what may be altered in the pathological context, we need to better understand these processes in the physiological context. Something that this work will now allow us to study.”, says Zita Santos.
In service to (human) medicine
“What is particularly inspiring”, says Bart Deplancke, “is how the fly community united over biological, technological and computational borders to generate this huge dataset and study all the different cell types in great detail, yielding perhaps the most highly curated cell atlas to date”.
“We are therefore convinced that our Fly Cell Atlas will constitute a valuable resource for the research community as a reference for studies of gene function at single-cell resolution,” says Norbert Perrimon from Harvard. “This will be helpful for anyone studying biological processes in flies but also for modelling human diseases at a whole-organism level with cell-type resolution.”
The consortium made all its data freely available online for further analysis through multiple portals or for custom analyses using other single cell tools.
“I am so pleased that the CZ Biohub was able to contribute to this monumental community resource,” says Stephen Quake from Stanford and the CZ Biohub. “We are excited that whole-organism cell atlases are now reaching fruition for a number of important organisms and are being made available to scientists across the globe.”