Case report: Compound heterozygous NUP85 variants cause autosomal recessive primary microcephaly

Abstract

Nucleoporin (NUP) 85 is a member of the Y-complex of nuclear pore complex (NPC) that is key for nucleocytoplasmic transport function, regulation of mitosis, transcription, and chromatin organization. Mutations in various nucleoporin genes have been linked to several human diseases. Among them, NUP85 was linked to childhood-onset steroid-resistant nephrotic syndrome (SRNS) in four affected individuals with intellectual disability but no microcephaly. Recently, we broaden the phenotype spectrum of NUP85-associated disease by reporting NUP85 variants in two unrelated individuals with primary autosomal recessive microcephaly (MCPH) and Seckel syndrome (SCKS) spectrum disorders (MCPH-SCKS) without SRNS. In this study, we report compound heterozygous NUP85 variants in an index patient with only MCPH phenotype, but neither Seckel syndrome nor SRNS was reported. We showed that the identified missense variants cause reduced cell viability of patient-derived fibroblasts. Structural simulation analysis of double variants is predicted to alter the structure of NUP85 and its interactions with neighboring NUPs. Our study thereby further expands the phenotypic spectrum of NUP85-associated human disorder and emphasizes the crucial role of NUP85 in the brain development and function.

Keywords: MCPH-SCKS; NUP85; brain development; microcephaly; speech disorder.

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Copyright © 2023 Ravindran, Lesca, Januel, Goldgruber, Dickmanns, Margot and Kaindl.

Figures

Figure 1

Phenotype of index patient with compound heterozygous NUP85 mutation. (A) Pedigree. (B) Pictures of affected individual (II.2). (C) MRI images of the head (sagittal) T2 images of II.2 shows reduced brain volume. (D) Representation of identified compound heterozygous variants by whole genome sequencing in the NUP85 cDNA c.454C > A in exon 6 (maternally inherited) and c.487C > A in exon 7 (paternally inherited) and NUP85 wild-type protein (p.L152I, p.L163I). (E) Mutations lie in the highly conserved region of the NUP85 protein across species. (F) Unchanged levels of total NUP85 protein in II.2-derived fibroblasts compared to controls [NUP85 (75kDa), actin (43kDa) (loading control)] (n = 3, one-way ANOVA, Tukey's multiple comparison test, p = 0.2973). (H) Cell viability in II.2-patient derived fibroblasts is significantly reduced compared to controls (n=8, one-way ANOVA, Tukey's multiple comparison test, ****p < 0.0001). (I) Structural overlay of human NUP85 based on PDBid 7R5K (purple) and the L152I/L163I double mutant (wheat). Top panel: Overlay of the overall structures; bottom panel: magnification of the hinge region (indicated by red line), the structures have been overlaid using the central region of the molecules. The mutations are located in this hinge region and are indicated in ball and stick mode. (J) Significant change of the interaction pattern due to mutations. Magnification of the interaction patterns as evaluated using the program Arpeggio under standard settings. Top panel wild-type, bottom panel-double mutant. The mutated residues are indicted in the colors as in (I).