Clinical Manifestations
General data, visual acuity results, fundus photographs, and FFA of 8 affected individuals including proband and first-degree relatives from 4 families were shown in Table 1. Among probands, there were 3 males and 1 female with a mean age of 12.25 years old (range, 7 to 17 years), while there were 1 male and 3 female of affected family members with a mean age of 43.25 years old (range, 42 to 45 years). The visual acuity ranged from finger count before the eye to 1.0. Fundus manifestations varied significantly among individuals even of the same family, 3/4 of the probands manifested as stage 3 while their parents were stage 2. Specifically, the FFA of the probands in three families exhibited RD in either of the eyes except for the proband from family 1 whose fundus only showed dilated blood vessels and fluorescein leakage, while their parents were consistent in showing no perfusion area, increased vascular branching and stained vascular walls. (Fig. 1).
Mutations Detected By Targeted Genetic Sequencing
Four mutations were identified in four out of nine (44%) families (Table 2). Among them, two heterozygous mutations (c.4289delC:p.Pro1431Argfs*8 and c.2073G > T:p.Trp691Cys) located in LRP5 were novel while the other two mutations (c.1801G > A:p.Gly601Arg in LRP5 and c.633T > A:p.Tyr211* in TSPAN12) have been reported previously. 32, 33
The novel mutation c.4289delC (p.Pro1431Argfs*8) in LRP5 resulted in the proline (Pro) at position 1431 being replaced by arginine (Arg) and premature termination at position 1437 after eight frameshift amio acids, which eventually led to a truncated protein product (Fig. 2A). The second novel mutation c.2073G > T (p.Trp691Cys) was found in family 2 and resulted in the tryptophn (Trp) at position 691 being replaced by cysteine (Cys) (Fig. 2A). These two mutations were absent in other healthy family members but detected in the probands and affected relatives.
Two mutations in LRP5 (c.1801G > A:p.Gly601Arg) and TSPAN12 (c.633T > A: p.Tyr211*) identified in families 3 and 4, respectively, have previously been reported as pathogenic. The heterozygous missense mutation c.1801G > A of LRP5 caused glycine (Gly) at position 601 replaced by arginine (p.Gly601Arg) (Fig. 2A). The heterozygous missense mutation c.633T > A of TSPAN12 caused nonsense mutations in amino acids (p.Tyr211*), resulting in a truncation of more than 30% of the protein (Fig. 2A).
Pathogenicity Analysis
Two mutations in LRP5 (c.4289delC: p.Pro1431Argfs*8 and c.2073G > T: p.Trp691Cys) and one mutation in TSPAN12 (c.633T > A:p.Tyr211*) were not observed in databases such as dbSNP, ExAC or 1000genomes, while the minimum allele frequency (MAF) of the mutation (c.1801g > A:p.Gly601Arg) was 0.0000083, Two of the mutations (c.2073G > T:p.Trp691Cys and c.1801g > A:p.Gly601Arg) were predicted to be disease-causing or damaging by in silico analysis methods SIFT, Polyphen-2, REVEL (scored 0.994, and 0.965 respectively), mutation taster and GERP++ (scored 4.11, and 4.13 respectively). The remaining two mutations (c.4289delC:p.Pro1431Argfs*8 and c.633T > A:p.Tyr211*) were predicted to be disease-causing or damaging by mutation taster and GERP++ (scored 4.53 and 5.68 respectively) (Table 2). All four variants were cosegregated with patients among family members and the sites are conserved in various species from humans to zebrafish (Fig. 2B). Therefore, all of these variations were considered pathogenic according to the ACMG standard.
Molecular Dynamic Simulation And Data Analysis
RMSD (root mean square deviation) and RMSF (root mean square fluctuation) are common measures of protein spatial variations in an MD simulation. RMSD describes the molecule’s overall discrepancy with respect to a reference conformation. The RMSD values of the wildtype and two mutations of LRP5 were depicted in Fig. 3A. Throughout the simulation, the structure of p.Trp691Cys was more stable than the wildtype and p.Pro1431Argfs*8 (P = 0.000, <0.05) while the backbone atoms of the three proteins may be maintained around 1.5nm.
RMSF, on the other hand, is a per atom quantity describing the atom’s variation over the whole trajectory. The RMSF values of the three proteins were shown in Fig. 3B that the highly active sites of wildtype were 10–27, 1318–1387, 1513–1520, and 1606–1615, while those of p.Trp691Cys were 14–15, 1331–1333, and 1486–1489, and those of p.Pro1431Argfs*8 were 1–28 and 1261–1385, indicating large differences in highly flexible sites among the three proteins. The flexible region of the p.Trp691Cys ensemble was smaller than that of the wildtype, and the overall structure was more convergent and rigid, while the p.Pro1431Argfs*8 ensemble showed more divergence and flexibility at the 1261–1385 residues. The changes in the active regions of the two mutant proteins were also shown in the 3D structure diagram in Fig. 3C. These results indicated that the two mutations had notable alterations in the LRP5 protein structure.
Rg values, which were used to examine the distance or fluctuation from c-α-atoms to the center of mass, were 4.34 Å, 4.25 Å, and 4.45 Å for the wildtype and two mutants, respectively (Fig. 3C). C-α-atoms fluctuated more in the p.Pro1431Argfs*8 mutant (P = 0.000, < 0.05), and less in the p.Trp691Cys mutant (P = 0.000, < 0.05) compared with the wildtype (Fig. 3D), indicating that the mutation may increase the stability of p.Trp691Cys and the flexibility of p.Pro1431Argfs*8.
HBNUM values, an index to reflect hydrogen bond numbers and protein structural stability, indicated that they had similar structural stability in p.Trp691Cys and wildtype, while the stability of p.Pro1431Argfs*8 was lower due to the absence of C-terminus structures (Fig. 3E). For intramolecular interactions through hydrogen bonds, as shown in Fig. 3F, the Trp691 formed hydrogen bonds with Ser700 in the wildtype, while the Cys691 of p.Trp691Cys formed hydrogen bonds with Ala677, Ala679, and Ser700. In the p.Pro1431Argfs*8 mutant, the Pro1431 was transformed into Arg, which formed hydrogen bonds with Tyr719, Glu721, and Thr737. The alterations in hydrogen bond distribution certainly contributed to the structural and conformational changes.
Then selected the last 50ns of the simulation for DSSP analysis and visualized the 3D structures and active sites by PyMOL (Figs. 4A and B) after the final structure reached convergence during the simulation. The DSSP results indicated the numbers of coils, turn, and a-helix increased but the number of b-sheet, bend, and 3-helix decreased in p.Trp691Cys, compared with those in the wildtype (Figs. 4C). The numbers of all secondary structures of p.Pro1431Argfs*8 were lower than those of wildtype (Figs. 4C).
Table 1
Summary of general Information and phenotype characteristics of affected individuals from 4 FEVR families
Family | Patients | Gender | Age at Initial visit | BCVA | FEVR Stage | FFA |
| | | | OD | OS | OD | OS | |
Family 1 | II2: | F | 9y | 0. 1 | 0. 4 | 2 | 2 | OU: Dilated blood vessels; fluorescein leakage |
| I2: | F | 42y | 1. 0 | 1. 0 | 2 | 2 | OU: no perfusion area; increased vascular branches; stained vascular wall |
Family 2 | II1: | M | 17y | 1. 0 | 0. 6 | 2 | 3 | OD: fluorescein leakage; no perfusion area OS: postoperative of RD |
| I2: | F | 45y | 0. 8 | 0. 8 | 2 | 2 | OU: no perfusion area; increased vascular branches |
Family 3 | II2: | M | 7y | 0. 2 | FC/BE | 2 | 3 | OD:paraoptic disc and temporal retinal atrophy, fluorescein leakage OS: RD and retinal fold |
| I1: | M | 43y | 1. 0 | 1. 0 | 2 | 2 | OU: no perfusion area; increased vascular branches; stained vascular wall |
Family 4 | II2: | M | 16y | 0. 5 | 0. 7 | 3 | 2 | OD: RD and fluorescein leakage OS: no perfusion area; increased vascular branches; fluorescein leakage |
| I2: | F | 43y | 1. 0 | 1. 0 | 2 | 2 | OU: no perfusion area; increased vascular branches; fluorescein leakage |
BCVA, Best corrected visual acuity; F, Female; FC/BE, finger count before the eye; FFA, Fundus fluorescein angiography; M, Male; OD, right eye; OS, left eye; OU, both eyes; RD: retinal detachment.
Table 2
Computational analysis of causative mutations in four probands with FEVR
Family | proband | Gene | ORF and Amino acid changes | Allele Status | MAF | SIFT | Polyphen-2 | REVEL | Mutation taster | GERP ++ | ACMG | Genetic Model | Ref | |
Family 1 | II2 | LRP5 | c.4289delC: p.Pro1431Argfs*8 | Het | NA | NA | NA | NA | DC | 4. 53 | Pathogenic | AD | Novel | |
Family 2 | II1 | LRP5 | c.2073G > T: p.Trp691Cys | Het | NA | D | PrD | 0. 994 | DC | 4. 11 | Pathogenic | AD | Novel | |
Family 3 | II2 | LRP5 | c.1801G > A: p.G601R | Het | 0. 0000083 | D | PrD | 0. 965 | DC | 4. 13 | Pathogenic | AD | Reported | |
Family 4 | II2 | TSPAN12 | c.633T > A: p.Tyr211* | Het | NA | NA | NA | NA | DC | 5. 68 | Pathogenic | AD | Reported | |
Notes: In silico analyses: SIFT, Polyphen-2, REVEL, and GERP ++.
Abbreviations: ACMG, American College of Medical Genetics and Genomics; AD, autosomal dominant inheritance; D, damaging/ deleterious; DC, disease-causing; Het, heterozygous; MAF, minimum allele frequency; NA, not available; ORF, open reading frame; PrD, probably damaging. Ref