A new map of human cilia reveals unexpected protein diversity

Tiny organelles hold big surprises. A new study published in Cell reveals unexpected diversity in cilia, with implications for biology and medicine.

Jan Hansen (HPA/SciLifeLab) has always been drawn to hidden worlds. In his case, the worlds are microscopic: the molecules and cells that quietly sustain life. That fascination led him to study Molecular Biomedicine in Bonn, where he discovered cilia. These hair-like projections are easy to miss, yet they play critical roles in human biology.

“These organelles are small, yet defects in them can have dramatic effects,” Hansen explains. “In rare cases, they can even lead to extra fingers.”

During his PhD, Jan focused on ciliary signaling pathways and developed tools to explore these tiny structures. But one question remained: how much do we really understand about the human primary cilium at a systems level? That curiosity brought him to Emma Lundberg’s lab at SciLifeLab and the Human Protein Atlas in 2022. In 2023, Hansen moved to the Lundberg lab at Stanford University, while continuing his close collaboration with the Human Protein Atlas at SciLifeLab.

A systems-level view of human cilia

The result is a striking new map of ciliary proteins, published in Cell. Using spatial proteomics, the research team charted over 700 proteins across different cell types. The findings surprised even them. Cilia are not uniform. Protein composition varies not only between cell types but also between individual cilia in the same cell. Ninety-one of these proteins had never been linked to cilia before.

“Each cilium is customized for its cell. That adaptability was something we had not fully appreciated before,” Hansen says.

The map is not just academic. In collaboration with clinicians, the team highlighted a candidate gene for ciliopathies, showing how these datasets can help interpret genetic conditions.

For Hansen, the work is more than discovery. It is the thrill of solving complex puzzles, collaborating across borders, and creating knowledge that can actually help people.

Next, he plans to investigate the functions of the new proteins and expand the Human Protein Atlas. These tiny organelles may be hidden, but the insights they offer could change how we understand cells and ourselves.

“Mapping cilia at this scale shows just how adaptable these structures are,” Hansen reflects. “It also reminds us that even the smallest parts of the cell can hold big clues for medicine and biology. There is still so much to uncover, and that’s what makes this work exciting.”

DOI: 10.1016/j.cell.2025.08.039

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