"Cellcode" of Life - Interview with a BGI researcher

Joint research involving BGI, Aarhus University, Karolinska Institutet and other partners published in Nature Communications covers the first transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. With this map, scientists are better able to understand the landscape of single-cell transcriptomes within diverse pig organs. 

This time, #ProudofYou has invited BGI senior researcher and Aarhus University associate professor, Yonglun Luo to share highlights of this research paper and share more details about why this team embarked upon this topic.

Pigs are valuable large animal models for biomedical and genetic research. The pig is also used for modeling both monogenic and complex human diseases such as cystic fibrosis and Huntington’s disease. Previous studies in pigs were restricted to a few tissues or a single organ. For cross-species organ transplantation (xenotransplantation), single-cell level understanding is vital to minimize the risk of rejection.

Pig genome research is part of a series of projects led by BGI, Aarhus University, and Karolinska Institutet (KI) from 2017 till now. The research team has presented an open-access pig expression map based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups before starting upon single-cell level research.

Q: In your opinion, what makes friendships between BGI and scientists involved in this research unique? 

Yonglun: Our friendship with Aarhus University and KI is built upon complementary capabilities and a shared mission. A few years ago, we kicked off this deep scientific collaboration on exploring the heterogeneity and functions of blood vascular endothelial cells in health and diseases by single-cell RNA sequencing technology with Aarhus University. We started the pig atlas collaboration with KI to better annotate the functions of pig cells, thus facilitating the use of pigs in biomedical research and applications.

Q： How do you feel when you get involved in working with such an international team?

Yonglun: The collaboration between BGI, KI and Aarhus University is very effective. BGI provides advanced sequencing platform technology. KI focuses on data analysis. Aarhus team provides insights into the biomedical applications. We make full use of each other’s strengths so that we can connect the dots better in our work.

Q： In your opinion, what more can we do together with our partners?

Yonglun: Life science has been developing at a high speed, which also makes it more competitive. BGI’s fast and accurate sequencing capabilities are key to the successes that we have achieved together with our partners. There are increasing demands for omics technologies for a better understanding of the highly complex genetic and molecular mechanisms in humans and other organisms, such as single-cell and spatial transcriptomics technologies, as well as data analysis.

While we continue providing better and faster sequencing supports, we should broaden our collaborations with our collaborative partners. For instance, we can provide early access to the new omics technologies developed by BGI, as well as provide training to young students, postdocs, and scientists on how to better handle and analyze the huge volume of data generated. 

Q: And how’s the research environment in Denmark? Does it affect your way of communicating with people?

Yonglun: I think it is a peaceful and happy country. Many people prefer to work collaboratively. The research atmosphere is very open, and you have time to think and create. This means that folks are more open to your occasional crazy ideas! It is also receptive to younger and female researchers who are encouraged to do more in line with their interests.

In addition, the research environment is more socially driven yet results oriented. When we start research, we think about what society needs. Our research should serve the public. For me personally, I feel we have more freedom while there’s also a need to deliver.

Q: How would you describe life in Denmark? Any further plans?

Yonglun: It is like a rainbow with active collaboration and a strong sense of social purpose. With the development of Stereo-seq, based on new technological platforms, I hope to get a better understanding of cellular functions relevant to disease and facilitate more multi-party collaboration to promote international scientific collaboration.

Well, that’s for today. We’ll see you next time!

References:

1. Sjöstedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, Oksvold P, Edfors F, Limiszewska A, Hikmet F, Huang J, Du Y, Lin L, Dong Z, Yang L, Liu X, Jiang H, Xu X, Wang J, Yang H, Bolund L, Mardinoglu A, Zhang C, von Feilitzen K, Lindskog C, Pontén F, Luo Y, Hökfelt T, Uhlén M, Mulder J. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. 2020 Mar 6;367(6482):eaay5947. doi: 10.1126/science.aay5947. PMID: 32139519.

2. Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol. 2022 Jan 25;20(1):25. doi: 10.1186/s12915-022-01229-y. PMID: 35073880; PMCID: PMC8788080.

3. Wang F, Ding P, Liang X, Ding X, Brandt CB, Sjöstedt E, Zhu J, Bolund S, Zhang L, de Rooij LPMH, Luo L, Wei Y, Zhao W, Lv Z, Haskó J, Li R, Qin Q, Jia Y, Wu W, Yuan Y, Pu M, Wang H, Wu A, Xie L, Liu P, Chen F, Herold J, Kalucka J, Karlsson M, Zhang X, Helmig RB, Fagerberg L, Lindskog C, Pontén F, Uhlen M, Bolund L, Jessen N, Jiang H, Xu X, Yang H, Carmeliet P, Mulder J, Chen D, Lin L, Luo Y. Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nat Commun. 2022 Jun 24;13(1):3620. doi: 10.1038/s41467-022-31388-z. PMID: 35750885; PMCID: PMC9232580.