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Updated: Jan 19, 2026

Quantitative PCR-based Assay to Measure Sonic Hedgehog Signaling in Cellular Model of Ciliogenesis
Published on: January 31, 2025
NRF2-dependent gene expression promotes ciliogenesis and Hedgehog signaling
Ana Martin-Hurtado1,2, Raquel Martin-Morales1,2, Natalia Robledinos-Antón1,2,3
1Alberto Sols Biomedical Research Institute UAM-CSIC and Department of Biochemistry, School of Medicine, Autonomous University of Madrid (UAM), Madrid, Spain.
Abstract:
The transcription factor NRF2 is a master regulator of cellular antioxidant and detoxification responses, but it also regulates other processes such as autophagy and pluripotency. In human embryonic stem cells (hESCs), NRF2 antagonizes neuroectoderm differentiation, which only occurs after NRF2 is repressed via a Primary Cilia-Autophagy-NRF2 (PAN) axis. However, the functional connections between NRF2 and primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae, remain poorly understood. For instance, nothing is known about whether NRF2 affects cilia, or whether cilia regulation of NRF2 extends beyond hESCs. Here, we show that NRF2 and primary cilia reciprocally regulate each other. First, we demonstrate that fibroblasts lacking primary cilia have higher NRF2 activity, which is rescued by autophagy-activating mTOR inhibitors, indicating that the PAN axis also operates in differentiated cells. Furthermore, NRF2 controls cilia formation and function. NRF2-null cells grow fewer and shorter cilia and display impaired Hedgehog signaling, a cilia-dependent pathway. These defects are not due to increased oxidative stress or ciliophagy, but rather to NRF2 promoting expression of multiple ciliogenic and Hedgehog pathway genes. Among these, we focused on GLI2 and GLI3, the transcription factors controlling Hh pathway output. Both their mRNA and protein levels are reduced in NRF2-null cells, consistent with their gene promoters containing consensus ARE sequences predicted to bind NRF2. Moreover, GLI2 and GLI3 fail to accumulate at the ciliary tip of NRF2-null cells upon Hh pathway activation. Given the importance of NRF2 and ciliary signaling in human disease, our data may have important biomedical implications.
Insights
Nuclear factor erythroid 2-related factor 2 (NRF2) and primary cilia mutually regulate each other. NRF2 impacts cilia formation and function, while cilia influence NRF2 activity in differentiated cells.
Area of Science:
- Cell Biology
- Molecular Biology
- Developmental Biology
Background:
- Nuclear factor erythroid 2-related factor 2 (NRF2) is a key regulator of cellular responses.
- Primary cilia act as cellular antennae, crucial for signaling pathways.
- The interplay between NRF2 and primary cilia is largely unexplored, particularly outside of human embryonic stem cells (hESCs).
Purpose of the Study:
- To investigate the reciprocal regulatory relationship between NRF2 and primary cilia.
- To determine if the Primary Cilia-Autophagy-NRF2 (PAN) axis functions in differentiated cells.
- To elucidate NRF2's role in primary cilia formation, function, and associated signaling pathways.
Main Methods:
- Utilized fibroblasts lacking primary cilia to assess NRF2 activity.
- Employed autophagy-activating mTOR inhibitors to rescue NRF2 activity.
- Analyzed cilia formation, length, and Hedgehog signaling in NRF2-null cells.
- Investigated the expression of ciliogenic and Hedgehog pathway genes, including GLI2 and GLI3.
Main Results:
- Fibroblasts lacking primary cilia exhibit elevated NRF2 activity, which is normalized by mTOR inhibitors, confirming the PAN axis in differentiated cells.
- NRF2 deficiency leads to reduced cilia number and length, and impaired Hedgehog signaling.
- NRF2 promotes the expression of genes essential for cilia formation and Hedgehog pathway function, including GLI2 and GLI3.
- Reduced GLI2 and GLI3 levels in NRF2-null cells are linked to NRF2 binding to their promoter regions.
Conclusions:
- NRF2 and primary cilia engage in a reciprocal regulatory loop.
- The PAN axis is functional in differentiated cells, linking cilia, autophagy, and NRF2.
- NRF2 is essential for proper cilia development and Hedgehog pathway signaling, potentially through regulating GLI transcription factors.
- These findings highlight the significance of NRF2 and ciliary signaling in human health and disease.
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