Molecular basis of nuclear pore formation

The National Institute of General Medical Sciences awarded Sanford Burnham Prebys Medical Discovery Institute $2,903,176 on September 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate the molecular mechanisms of nuclear pore complex formation.

The project, titled "Molecular Basis of Nuclear Pore Formation," will define regulatory principles governing nuclear pore biogenesis in mammalian cells. The research addresses how alterations in nuclear pore number and integrity contribute to cellular aging and human disorders including Alzheimer's disease, amyotrophic lateral sclerosis, premature aging, and cancer. The work builds on a whole-genome siRNA screen that identified two unexpected pathways controlling nuclear pore assembly: lipid metabolism and RNA splicing. Aim 1 will determine how ceramides promote nuclear pore formation through membrane bending, microdomain formation, and nucleoporin recruitment. Aim 2 will examine how the splicing factor SRSF3 regulates assembly of nucleoporins, particularly NUP98/NUP96, and will investigate a novel splicing mechanism determining NUP98 localization to nuclear pores or association with the genome.

Work is performed in La Jolla, California. The period of performance runs from September 1, 2026, through August 31, 2030.

Abstract

Nuclear pore complexes (NPCS) are essential protein assemblies that control selective transport between the nucleus and cytoplasm, acting as guardians of the genome. NPC assembly and composition are precisely regulated, and alterations in NPC number and integrity are associated with cellular aging and several human disorders, including neurodegenerative diseases such as alzheimer's (ad) and amyotrophic lateral sclerosis (ALS), premature aging, and cancer. Despite the critical importance of nuclear pores for maintaining cellular homeostasis and their connections to disease, the molecular mechanisms that regulate NPC biogenesis in mammalian cells remain poorly understood. To address this GAP, we recently conducted a whole-genome sirna screen to systematically identify factors that control NPC assembly. This unbiased approach revealed unexpected roles for two pathways: lipid metabolism and RNA splicing. Specifically, we discovered that enzymes regulating ceramide production and the splicing factor SRSF3 are critical for NPC formation. Our preliminary studies suggest that ceramides may act during the early steps of NPC biogenesis by altering nuclear membrane organization and promoting nucleoporin recruitment, while SRSF3 controls the splicing of the NUP98/NUP96 transcript, producing isoforms with distinct roles in NPC assembly and intranuclear genome regulation. Building on these discoveries, this proposal seeks to define new regulatory principles of NPC biogenesis. In aim 1, we will determine how ceramides promote NPC formation, focusing on their roles in membrane bending, microdomain formation, and nucleoporin recruitment. In aim 2, we will dissect how SRSF3-mediated splicing of nucleoporin transcripts, particularly NUP98/NUP96, regulates NPC assembly. As part of this aim, we will also investigate a novel splicing mechanism determining NUP98 localization to NPC or association with the genome, which represents a previously unrecognized mode of nucleoporin function regulation. By integrating lipid biology, RNA splicing, and nuclear pore assembly assays, this research will uncover new regulatory mechanisms of NPC biogenesis. Beyond advancing our fundamental understanding of NPC formation, this work has important translational implications. Dysregulated ceramide metabolism is a well-established feature of ad pathology and progression and known a driver of neurodegeneration, which are linked to loss of NPC function, while SRSF3 is frequently upregulated in cancer, where NPC numbers are increased. These two factors, which we identified as regulators of NPC assembly, are thus already linked to the very diseases most closely associated with pore dysfunction. By establishing ceramides and SRSF3 as central regulators of NPC assembly, this project could expose new therapeutic opportunities for these diseases and other pathologies driven by nuclear transport alterations.