The people behind the papers – Christopher De Bono, Stéphane Zaffran and Heather Etchevers

Christopher De Bono (left), Stéphane Zaffran (middle) and Heather Etchevers (right)

Heather and Stéphane, what questions are your labs trying to answer?

HE: Stéphane and I both come from a fundamental developmental biology background, but converged around 15 years ago on the same rare disease research unit with the French National Institutes of Health (INSERM), hosted at Aix Marseille University. The unifying theme of Marseille Medical Genetics is to understand mechanisms of a selection of rare diseases in order to offer new ways to diagnose, improve quality of life and treat affected patients. My lab has a long-standing interest in onset of neurocristopathies, diseases imputable to problems arising in the neural crest cell lineage, which often include congenital heart malformations, even though the heart is mostly a mesodermal structure.

SZ: As a developmental biologist, I am interested in the molecular and cellular mechanisms that control normal and pathological heart development. Congenital heart defects (CHDs) are the most common birth defects, and I believe it is important to provide answers regarding their origins. Therefore, my lab, within Marseille Medical Genetics (a center affiliated with both Aix Marseille University and INSERM), has established collaborative projects with clinicians to understand the genetic and environmental causes of these malformations. We focus on cardiac progenitor cells (including the second heart field) and neural crest-derived cardiac cells, both of which are known to be involved in CHDs. Like Heather, I am interested in neurocristopathies that affect the head and heart regions.

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

CDB: I first met Stéphane when I was a PhD student at Aix Marseille University. I was particularly interested in his work on the role of Hox genes and retinoic acid signaling in embryonic heart development. At the time, we collaborated and published articles on this topic. After completing my postdoc in New York, where I acquired skills in generating and analyzing single-cell RNA-sequencing data, and a strong knowledge of the cardiac neural crest cells, I joined Stéphane's laboratory to pursue my research in cardiac developmental biology. I am using single-cell and spatial transcriptomic cutting-edge technologies to uncover the mechanisms governing embryonic heart formation. Since the beginning of my scientific career, I have been fascinated by the study of the mechanisms controlling embryonic development, in particular cardiac development. I am especially focused on understanding how different cardiac stem cells contribute to different parts of the heart and how they communicate with their micro-environment to make proper contributions during embryogenesis. These questions continue to drive my research. Addressing these questions not only improves our knowledge of how the heart is formed but also helps us understand the origins of congenital heart defects.

Tell us about the background of the field that inspired your work

CDB, HE & SZ: While research on animal models has advanced our understanding of how vertebrate hearts form, our knowledge of human cardiac development remained largely limited to anatomical illustrations found in textbooks. Gaining access to human samples has, therefore, been a valuable resource, allowing us to expand our understanding of the specific features of human heart development. One of our collaborators, Alain Chédotal, had been involved in early elaboration of the Human Cell Atlas (https://www.humancellatlas.org/) and, with incitation from our national institution (INSERM), we began a French Human Developmental Cell Atlas (HuDeCA) in the same community spirit. As a partner in this program, we collaborated to better understand human heart development during the first trimester by identifying each cell type that participate in the formation of this organ. This had been broached in some pioneering work, but as developmental biologists using animal models, we were aware that rare cell populations we expected to find have not yet been sampled or characterized.

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

CDB, HE & SZ: An atlas is a tool that documents the frontiers of exploration at the time it is published. A cross between a map and an encyclopedia, it organizes and connects data and metadata of all kinds, and at scales only limited by the imagination. Atlases point us to the places where ‘hic sunt dracones’ (‘here be dragons’, referring to unexplored places); they orient present and future scientists. We are familiar with histological or embryo staging atlases. Here, we carefully mapped what types of cell exist and where they are in the fetal human heart in an early, critical window of developmental time. Our atlas presents nearly 50,000 single-nucleus transcriptomes enriched with spatial transcriptomic data from fetal hearts and integrated with existing datasets on human embryonic heart development. To validate our findings, we visualized transcripts and proteins with RNAscope and immunofluorescence staining. This comprehensive analysis identifies previously unrecognized cell types and states, including distinct subpopulations of cycling cardiomyocytes and anatomically specialized stromal cells, as well as a common cardiomyofibroblast progenitor. By integrating anatomical and molecular data, we linked positional features like innervation, conduction and atrioventricular septum subdomains to specialized cardiac functions. Furthermore, whole-mount light-sheet imaging provided a detailed view of the vascular and neural architecture within the developing human heart – all data that could be combined with other sets and re-analyzed. Together, we established an atlas of unprecedented spatial and temporal resolution, offering novel insights into some human-specific aspects of early heart development.

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

CDB: During our research, we generated single-nucleus RNA-sequencing data for transcriptomic information about all the cell types of the developing heart, but devoid of landmarks. Due to the similarity in the transcriptomes of certain cardiac cell types and the lack of information about their location within the heart, it was difficult to label them with certainty. On the other hand, we also generated spatial transcriptomic data that allowed us to define serial sample transcriptomes of different cardiac regions, but without cellular-level resolution. After testing several bioinformatic approaches, we finally succeeded in combining the two types of data. The result was data of unprecedented resolution, enabling us to finally study the transcriptomes at the single-cell level of precisely localized cells in fetal human hearts. It allowed us to identify and explore rare cardiac cell populations. At that moment, I knew that our study had reached an entirely new level.

Why did you choose to submit this paper to Development?

HE: Both Stéphane and I (and other co-authors) published some of our earliest papers in Development and have always felt it to be a journal for work that will stand the test of time. It seemed to be a good venue to show that developmental biologists can make meaningful contributions to the Human Cell Atlas, and we hope they and others will build on our findings.

SZ & CDB: We chose to submit our paper to Development because of its strong reputation for publishing high-impact research in developmental and stem cell biology. Given the journal's emphasis on fundamental mechanisms of organogenesis and its commitment to advancing our understanding of human development, Development was the ideal journal for our study. We wanted our findings to reach a broad audience of developmental biologists, stem cell researchers and cardiovascular scientists – many of whom look to Development for cutting-edge discoveries in the field. Finally, we appreciated the journal's rigorous, efficient and constructive peer review process, which helped refine and strengthen our study.

Christopher, what is next for you after this paper?

CDB: I will pursue my research on understanding the mechanisms that regulate mammalian heart formation. I aim to secure a tenured position in academic research, where I can further investigate embryonic heart development and lead my own projects in this field.

Heather and Stéphane, where will this story take your labs next?

HE: I'd like to use these and other ‘-omics’ techniques to learn more about the developing human cardiac autonomic system, and about specific functional effects in directed differentiation systems in vitro or in rare tumor predisposition syndromes.

SZ: Our recent findings have provided a solid base for understanding the cell types involved in human heart development. Building on this dataset, we now aim to investigate hearts with CHDs, such as atrioventricular septal defects or outflow tract anomalies, which are frequently observed at birth and often associated with chromosomal abnormalities. Advances in corrective surgery have enabled children with CHDs to reach adulthood and lead normal lives. However, those who undergo surgery for a CHD at birth face a higher risk of developing cardiovascular disease later in life. Our project will identify the specific cell types affected by these conditions to help understand why heart function may deteriorate in adulthood.

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

CDB: I like spending time with my family, especially hiking with my children. We are lucky enough to have the Calanques National Park nearby. I also enjoy wildlife photography and riding my bike to explore the mountains around my place. The south of France is an ideal location for this.

HE: I enjoy making music with other people. I've played clarinet since the age of 8, and am in a wind ensemble (Harmonie Municipale d'Aix-en-Provence, hmap.fr) that celebrated its centennial in 2012 and performs a dozen or so concerts a year. I also sing with the French-American Vocal Arts ensemble to introduce diverse influences on American music to French audiences, and perform using appropriate pronunciation and vocal technique for each era.

SZ: I enjoy learning about the world around me. I stay informed about politics, economics and environmental issues, as I believe these factors shape our future. I am particularly interested in sustainability and the challenges our society faces in preserving the planet for future generations. The well-being of our children and the world they will inherit is something I deeply care about.