Pioneering Lung Epigenomics

Xin Sun's Contributions to Functional Genomics

Center for Epigenomics collaborator Xin Sun is a Professor in Pediatrics and Cell and Developmental Biology at UC San Diego and serves as the Director of the Center for Lung Research and Innovation, a cross-campus initiative. Her research is at the forefront of lung genomics, harnessing single-cell and spatial genomics to profile the human lung. Sun has built a robust network of collaborations, including significant partnerships with NIH-funded projects such as LungMap — a partnership with C4E’s Allen Wang and Quan Zhu.

“My team is very fortunate to partner with C4E,” says Sun. “In the last five years, we have made a name for ourselves as the collaborative team that brings in single cell as well as spatial transcriptomics to the lung community.”

Sun's decision to move her lab from the University of Wisconsin-Madison, to UC San Diego in 2016 was driven by her desire to access the advanced genomic technologies such as single-cell sequencing — then in their early stages of development. This move proved timely, as the establishment of the Center for Epigenomics (C4E) shortly thereafter opened up new avenues for her research. Sun's lab is strategically located next to the center, fostering early and productive collaborations that have had a transformative impact on her research directions.

Her lab specializes in functional genomics, taking the hypotheses generated from lung profiling and validating them using mouse models and cell-based systems.

“You will see signatures of that in many publications over the last few years,” says Sun. “In the testing system, we use the single cell approaches to phenotype outcomes of mutants or over-expression of a gene that we generated. It really has quite a widespread impact.”

These efforts have been instrumental in several high-impact publications, including a 2020 eLife paper that applied single-cell lung data to profile COVID-19 receptors and susceptibility factors. Additionally, Sun's lab published a Nature paper on neural circuits that regulating lung response to allergen, utilizing single-cell analysis of the mouse brain in collaboration with the bioinformatics expertise of Wang and C4E’s Nathan Zemke.

“There is no question that we benefited from the strengths of the bioinformatics team,” adds Sun. “The team has a lot of expertise in epigenomics and transcriptomics and to have their eye on the data is amazing.”

What further sets Sun's lab apart is its strong integration with clinical research. Through partnerships with UC San Diego’s biobanking team and surgeons, her lab has banked high-quality human lung tissue for analysis. This synergy between basic and clinical research is also evident in her mentorship of physician scientists like Dr. Elizabeth Duong, an assistant professor in Pediatrics. Duong’s work in single-cell lung research is a testament to the interdisciplinary training fostered in the Sun lab and C4E, where clinicians and basic researchers collaborate to apply cutting-edge technologies to patient care.

Dr. Gaulton's collaboration with the Center for Epigenomics extends beyond type 1 diabetes. His team works on numerous projects related to other diseases and tissues, benefiting from the center's intimate knowledge of experimental techniques. The expertise in processing tissues, troubleshooting, and ensuring high-quality data is invaluable for advancing research. One notable project involves studying cystic fibrosis-related diabetes, where the team had to optimize single-cell assays for severely diseased pancreatic tissue.

Sun’s approach represents a holistic model of research, where technology, clinical insight, and basic science converge to advance understanding and treatment of lung diseases.