Freedman Lab Explores the Role Cilia Play in Signaling, Cell Fate, and Disease Development

cilia-free kidney organoids floating in 6 well plates
Cilia-free kidney organoids floating in well plates. Credit: Benjamin Freedman

The term cilia may stir high school biology memories of tiny hair-like structures used by single-celled organisms to swim the peaceful waters of Petri dishes. You are remembering that right. Propulsion is one purpose of motile cilia, which are found throughout the animal kingdom – from microscopic paramecia to fully-grown humans.

However, there is much more to these complex organelles. We know now that cilia come in several varieties, and each is vital for development and survival. Motile cilia, beating in waves, allow eukaryotic creatures to move, and help humans and other mammals clear mucus from their lungs, steer food through the digestive system, and push eggs from the ovary to the uterus.

Scientists have known about immotile (or primary) cilia since the late nineteenth century but often dismissed this type of cilia as vestigial structures that were left over from a time when cells needed a way to get around in watery environments. In fact, recent discoveries have revealed that primary cilia function as an antenna in most vertebrate cell types, enabling cells to receive and transmit signals from the environment and with other cells.

Engineering cells without cilia reveals insights with ramifications for human health.

Headshot of Beno Freedman
ISCRM faculty member Benjamin Freedman, PhD

Now, a new paper from the lab of ISCRM faculty member Beno Freedman, PhD, Associate Professor of Medicine/Nephrology, details a new tool that combines gene-editing and stem cell technologies to help researchers explore the role cilia play in a wide variety of diseases. ISCRM faculty member Hongxia Fu, PhD, is also an author of the study, which was published in the journal Nature Biomedical Engineering.

In their investigation, Freedman and his team used CRISPR gene-editing technology to create a line of cells that have the self-renewing and pluripotent qualities of stem cells, but lack a primary cilium. Freedman emphasizes this is not a condition that would normally exist in nature; we need cilia to survive. But, in the lab, engineering cells without cilia revealed several intriguing insights with ramifications for human health.

Primary cilia (red) lining the surface of human kidney organoids (gray)
Primary cilia (red) lining the surface of human kidney organoids (gray). Credit: Benjamin Freedman

One finding relates to a disease that the Freedman Lab studies closely – Polycystic Kidney Disease (PKD). In their ongoing research, the lab recreates PKD in kidney organoids by targeting specific genes associated with the disorder, an approach that does not affect the cilium. Now, they have shown it is possible to model PKD by disrupting the cilium, while leaving those genes alone. The fact that both paths lead to cysts further implicates cilia in disease development.

According to Freedman, the study also generated revelations about the hedgehog signaling pathway, which regulates stem cell differentiation. “Knocking out cilia disrupted hedgehog and taught us something new about hedgehog and kidney formation,” says Freedman. “What we saw is that cilia are really important for getting cells to go the final step toward becoming a kidney cell or brain cell, for example. And that seems to go through hedgehog. This matters for our research because we can’t understand PKD and ciliopathies without understanding the cilia and the pathways that function through cilia, including hedgehog.”

More broadly, Freedman is also excited about having a new way to take stem cells through the stages of human embryonic development without cilia, an experiment that would not be feasible otherwise, but that will allow his team and other researchers to better understand fundamental biological processes. For example, Freedman would like to explore how cilia influence the determination of a right side and left side in our bodies and to analyze molecules that may have therapeutic potential for PKD and hedgehog-related disorders.


Studies were supported by an Institute for Stem Cell and Regenerative Medicine Innovation
Pilot Award; Lara Nowak-Macklin Research Fund; NIH Awards R01DK117914 (B.S.F.),
UG3TR000504 (J.H.), UG3TR002158 (J.H.), UC2DK126006 (S.S.), K25HL135432 (H.F.)
and U01DK127553 (B.S.F.); the Northwest Kidney Centers; and start-up funds from the
University of Washington.