Novel variations in the PLOD1, COL1A1, COL5A2 and COL4A1 genes related to keratoconus

Abstract

Purpose: To investigate the genetic characteristics of four Chinese families affected by keratoconus (KC).

Methods: In the four families affected by KC, medical records, clinical observations, and blood samples were collected from all individuals. One hundred subjects without KC served as healthy controls. All controls and subjects in the four families underwent whole exome sequencing of their genomic DNA and polymerase chain reaction to confirm the variants. All variants were analyzed using online software; and in silico predictions of three-dimensional protein structures were performed.

Results: The clinical manifestations in those first-degree family members of the probands were atypical. The following four variants were identified in the four probands and other family members with KC: heterozygous missense variation c.109G>A (p.Glu37Lys, rs369263247) in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) gene; heterozygous missense variation c.3766G>A (p.Ala1256Thr, rs148216434) in the collagen type I alpha 1 (COL1A1) gene; heterozygous missense variant c.4364G>A (p.Gly1455Glu) in the collagen type V alpha 2 (COL5A2) gene; and missense variation c.976G>A (p.Glu326Ser) in the collagen type IV alpha 1 (COL4A1) gene. The above genotypes were co-segregated with corresponding phenotypes. All variations in these families appeared to be pathogenic.

Conclusion: Four variants in the PLOD1, COL1A1, COL5A2, and COL4A1 genes were identified in this study, which are collagen-coding genes and collagen crosslink regulatory genes and may be associated with the origin and development of KC. This study updates the knowledge of genes related to KC and the biomedical implications.

Keywords: 2-oxoglutarate 5-dioxygenase 1 (PLOD1); collagen type I alpha 1; collagen type IV alpha 1; collagen type V alpha 2; early diagnosis; keratoconus; procollagen-lysine.

FIGURE 1

Pedigrees of the Chinese families with keratoconus. (a) family 1; (b) family 2; (c) family 3; and (d) family 4. The squares represent the males, and the circles represent the females. The open symbols indicate the unaffected family members. The solid symbols indicate the infected individuals. The diagonal line indicates the family member who passed away. The arrows indicate the probands.

FIGURE 2

Corneal topography (Pentacam) reports show the mean values of posterior elevation of the cornea, maximum anterior surface curvatures, and central corneal thicknesses. (a) Proband (II.2) in family 1; (b) Proband (III.2) in family 2; (c) Proband (Ⅳ1) in family 3; (d) Proband (II.1) in family 4.

FIGURE 3

Sequence chromatograms of the variants. (a) c.109G>A (p.Glu37Lys, rs369263247) in PLOD1 gene (arrow); (b) a heterozygous missense variation c.3766G>A (p.Ala1256Thr, rs148216434) in COL1A1 gene (arrow); (c) a missense variation c.976G>A (p.Glu326Ser) in COL4A1 gene; (d) a heterozygous missense variant c.4364G>A (p.Gly1455Glu) in COL5A2 gene.

FIGURE 4

Three dimensional (3D) structures of the proteins show the sites of variants. The insert pictures are regional enlargements of the variants. (a) 3D modeling of wild-type PLOD1 and p.Glu37Lys variant. (b) 3D modeling of wild-type COL1A1 and p.Ala1256Ter variant. (c) 3D modeling of wild-type COL4A1 and p.Glu326Ser variant; (d) 3D modeling of wild-type COL5A2 and p.Gly1455Glu variant.

FIGURE 5

Protein–protein interaction (PPI) network. (a) the interaction of PLOD1 with COL1A1, COL4A1, and COL5A2; (b) the interaction of COL4A1 with ITGA and ITGB; (c) the interaction among COL1A1, COL1A2 and CO5A1, and their interaction with ITGB.

FIGURE 6

(a) p.Ala1256Ter amino acid change in COL1A1 located in the COLFI domain (arrow indicates 1,228–1,464aa); (b) p.Gly1455Glu in COL5A2 located in the COLFI domain (arrow indicates 1,265–1,499aa); (c) p.Gly326Ser in COL4A1 located in the Pfarm collagen domain (arrow indicates 273–334aa).