Junyue Cao Redefines Aging at the Cellular Level

Back in 2020, Rockefeller University cell biologist Junyue Cao set out to study the aging process using highly scalable single-cell genomic methods that he had previously created to study developing organisms.^1,2 These technologies, which then allowed him to track millions of individuals cells across the body to understand how and why organisms age, got our attention, and we featured Cao’s research in 2022.

To honor The Scientist 40^th anniversary, we interviewed Cao again to see how his work on the genomics of aging has evolved. He believes a lot has changed since The Scientist first spoke to him. Back then, Cao had just set up his own laboratory and was learning how to be a team leader and a mentor—and seeking guidance from his past mentors and faculty colleagues on how to do that. Over the past four years, Cao has been guiding a number of young researchers. The team has improved their single-cell genomic tools to uncover genetic and epigenetic dynamic changes during aging, reframing what scientists know about the process.

Cellular Aging: Everywhere, Synchronized, All at Once

Techniques such as single-cell transposase-accessible chromatin high-throughput sequencing (ATAC-seq) made it possible to map regions of the DNA that are accessible to the transcription machinery. But research using such methods mainly focused on one tissue or organ at a time, leaving Cao and others wondering how age could affect chromatin accessibility in cells across the entire organism.

To address this question, Cao and his team optimized an ATAC-seq technique developed by Jay Shendure, a geneticist at the University of Washington and Cao’s PhD mentor. The new method, dubbed EasySci-ATAC, enabled the researchers to assess age-related changes in chromatin accessibility and cell populations across multiple tissues of male and female mice at different life stages.^3,4

An illustration depicting different types of brain cells. — Using single-cell genomic strategies enabled researchers to identify dynamic changes associated with aging in hundreds of cell types in the brain.
Cao lab, The Rockefeller University

Aging is associated with increases or decreases in cell population numbers, with these patterns showing life stage specificity, that is, some cell groups expanded only in aged mice, while others were markedly depleted in young animals.⁴ This, Cao said, reveals how “aging is not one process, but it can be separated into different stages. For each stage, there is a specific group of cells that changes.”

The team also found that some cell subsets showed similar patterns across multiple tissues, indicating that aging may trigger coordinated cellular processes in different organs. What’s more, these cellular dynamics differed between female and male animals, a finding that could help explain why men and women differ in their vulnerability to diseases. Moving forward, Cao plans to explore the triggers of these age-related sex differences to determine if they are caused by extrinsic factors, such as sex hormones, or by chromatin differences between males and females.

The Origins of Age-Related Cell Population Shifts

While Cao’s EasySci-ATAC enabled the researchers to create a large-scale single-cell atlas of mammalian cell aging, uncovering why these cell population changes happened in the first place became the next question. His team devised TrackerSci, a technique that combines single-cell transcriptomics or chromatin accessibility profiling with click chemistry to tag newly produced DNA. Using this method, the researchers monitored gene expression and epigenetic changes of proliferating cells across an entire organ.⁵

In a proof-of-concept work, Cao and his team showed that they could use the method to profile the single-cell transcriptome or chromatin accessibility changes of almost 15,000 newborn cells in the mouse brain at different life stages.⁵ “It can basically give you the dynamic map across hundreds of different cell types,” Cao explained.

With TrackerSci, they detected hard-to-track progenitor cell populations that traditional proliferation assays frequently miss. They also found that proliferation of some cell populations increases or decreases during aging, calling into question the idea that the self-renewal and regenerative capacity of progenitor cells only decline with age.

More recently, Cao’s team expanded the use of TrackerSci to other organs by applying the strategy to 21 different tissues of young, adult, and aged mice.⁶ By monitoring newborn cells, the team found that cell population depletions or expansions are due to different paths that proliferating cells take during aging. While population reduction can be explained by lower cell renewal, global shifts in cell composition redistributes proliferating cells across different cell types, driving expansion of certain cell groups.

A Collaborative Effort

Reflecting on his work, Cao recognizes the potential that the single-cell genomic techniques he has developed hold for fields beyond aging. “For every new technology, we include very detailed step-by-step protocols and computation scripts so people can easily adapt them to their own labs,” Cao said. “What we are working on can potentially not only benefit our own interest but can be applied to many other areas, and I feel pretty excited about [that].”

Scientific advances and successes are not a one-man show, and Cao acknowledges the support he received from his colleagues, former mentors, and trainees who helped him to take his research ideas off the ground. “I don't think we [could] achieve any of this without that support,” he said.

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