Single Tissue Snapshot Reveals Biological Processes Unfolding Over Time

A core challenge in biology is understanding how processes in the body, such as cellular development and regeneration, unfold over long stretches of time, making them notoriously difficult to view at the molecular level. Now, a team led by researchers at Caltech has shown that a single snapshot of a mouse testis is enough to reconstruct the entire weeks-long cycle of sperm production, along with the cell-to-cell coordination that organizes it.

The key lies in using the spatial organization of the tissue. Each testis is essentially a tightly packed bundle of long tubes called seminiferous tubules, and sperm production unfolds inside them as a slow periodic cycle, known as the seminiferous epithelial cycle.

"Because each tubule cycles independently, a snapshot of the tissue catches different tubules at different stages, like frames from a movie scattered around a room," says Arun Chakravorty (PhD '25), a student in the MD-PhD joint program between Caltech and the David Geffen School of Medicine at UCLA. "Instead of following one tubule through time, we showed that by putting hundreds of tubule snapshots in the right order, we can reconstruct the whole cycle."

Chakravorty, who worked with Caltech's Long Cai, a professor of biology and biological engineering, is the first author of a recent paper in Cell that outlines their approach and findings.

Cai is known for developing seqFISH (sequential fluorescence in situ hybridization), an imaging technology that allows researchers to simultaneously visualize the expression of tens of thousands of different genes in cells across a tissue sample. Using this method, the team profiled more than 2,500 genes in over 800,000 single mouse testis cells. The same strategy, the team suggests, could open a window into many slow biological processes, from hair follicle regeneration to intestinal renewal.

"With preserved spatial information, you start to see how cells coordinate with each other," Cai says. "That's where a lot of the interesting biology can be discovered using new tools."

The study did more than demonstrate a new way to read time from a snapshot of tissue. One revelation centered on Sertoli cells, which surround and nurse the germ cells that give rise to sperm. Sertoli cells had long been known to shift their gene expression as the surrounding germ cells progressed through the cycle, but whether they were following the germ cells or keeping their own time was an open question.

"The assumption has been that the timing of spermatogenesis is dictated by germ cells," Chakravorty explains. "But when we examined testes depleted of germ cells, we found that Sertoli cells kept cycling on their own. They have their own intrinsic rhythm. It's weaker on its own, but as germ cells develop, they reinforce this rhythm and the cycle becomes much more robust."

The team also identified what sustains the intrinsic clock in Sertoli cells: retinoic acid, a signaling molecule derived from vitamin A. When the team blocked retinoic acid production, Sertoli cells stalled mid-cycle, showing that retinoic acid is required to keep the intrinsic clock running.

"The seminiferous cycle is a beautiful phenomenon that has fascinated generations of researchers," says Shosei Yoshida, a professor at the National Institute for Basic Biology in Japan who is an expert on spermatogenesis and a co-corresponding author of the paper. "I am delighted to have contributed to this study, which offers a new molecular view of this classic process. I look forward to seeing how this work will inspire broader insights into dynamical tissue homeostasis."

Indeed, the paper's findings hint at broader principles, particularly that intrinsic oscillators—such as the one found in Sertoli cells—may coordinate tissue architecture and timing across many systems, Cai says.

Chakravorty adds that this discovery reframes how scientists think about developmental coordination. "The cells undergoing the most visible transformations have generally been assumed to drive timing," he says. "What we see here suggests the rhythm can originate in the surrounding environment as well."

Chakravorty and Cai note that understanding complex systems requires expertise spanning disciplines, and they would not have been able to make their discoveries without Yoshida and Ben D. Simons, a professor at the University of Cambridge who works on stem cell dynamics and was also a co-corresponding author of the paper.

"It was exciting to be part of a multidisciplinary team, showing how such elegant and advanced spatial-profiling technologies can unlock the programs controlling sperm production," Simons says. "These findings question whether parallel mechanisms control stem cell dynamics in other epithelial tissue contexts."

Chakravorty, now in the clinical portion of his joint MD-PhD program, is already thinking about next steps. "Identifying similar architectures in other systems would suggest a general principle of tissue organization," he says. "Understanding how that coordination fails is where this work connects to clinical applications. Now that we are beginning to understand how coordination occurs, I want to understand what happens when it breaks."

The Cell paper is titled "The temporal architecture of the seminiferous epithelial cycle revealed by spatial transcriptomics." Additional Caltech authors are Jina Yun, lab manager and scientific researcher; Henry Amrhein, genomics information specialist; and Katsuya L. Colón (PhD '25), formerly of the Cai lab. Toshiyuki Sato, a research fellow in Yoshida's lab, also contributed to the study. The research was supported by the Caltech-affiliated Allen Discovery Center for Cell Lineage Tracing, the National Institutes of Health, the Japan Agency for Medical Research and Development, and a David Geffen Medical Scholarship.