Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers

• Published in: Communications biology Vol. 6; no. 1; p. 1033
• Main Authors: Neely, Amy E., Zhang, Yang, Blumensaadt, Laura A., Mao, Hongjing, Brenner, Benjamin, Sun, Cheng, Zhang, Hao F., Bao, Xiaomin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.10.2023; Nature Publishing Group; Springer Nature; Nature Portfolio
• Subjects: 13; 13/1; 13/100; 13/106; 13/109; 13/2; 13/89; 14; 14/1; 14/19; 38; 631/136/2441; 631/80/389/2029; 82; 82/80; Active Transport, Cell Nucleus; Antibodies; BASIC BIOLOGICAL SCIENCES; Biology; Biomedical and Life Sciences; Cell culture; Cytoplasm; Down-Regulation; ENVIRONMENTAL SCIENCES; Gene expression; Humans; Keratinocytes; Life Sciences; Localization; Membrane permeability; NF-kappa B - metabolism; NF-κB protein; Nuclear Pore - genetics; Nuclear Pore - metabolism; Nuclear Pore Complex Proteins - genetics; Nuclear Pore Complex Proteins - metabolism; Nuclear pores; Nucleoporins; Permeability; Proteins; Stochasticity; Transcription factors; Transcriptomes
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-05398-6

Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes’ clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers. Nucleoporins (NUPs) compose the nuclear pores. As skin epidermal cells switch from the progenitor state to differentiation, NUPs are downregulated without changing pore numbers. Downregulation of NUP93 is further connected to NF-kB activation.