Autosomal recessive LRP1-related syndrome featuring cardiopulmonary dysfunction, bone dysmorphology, and corneal clouding

Abstract

We provide the first study of two siblings with a novel autosomal recessive LRP1-related syndrome identified by rapid genome sequencing and overlapping multiple genetic models. The patients presented with respiratory distress, congenital heart defects, hypotonia, dysmorphology, and unique findings, including corneal clouding and ascites. Both siblings had compound heterozygous damaging variants, c.11420G > C (p.Cys3807Ser) and c.12407T > G (p.Val4136Gly) in LRP1, in which segregation analysis helped dismiss additional variants of interest. LRP1 analysis using multiple human/mouse data sets reveals a correlation to patient phenotypes of Peters plus syndrome with additional severe cardiomyopathy and blood vessel development complications linked to neural crest cells.

Keywords: episodic respiratory distress; fetal ascites; hypertelorism; mild fetal ventriculomegaly; patent ductus arteriosus after premature birth; polyhydramnios; postductal coarctation of the aorta; small anterior fontanelle.

Figure 1.

The low-density lipoprotein (LDL) receptor family and development. (A) Sequences with an E-value <1 × 10⁻²⁰ based on BLAST of human LRP1 protein (red box). Sequences were aligned with the MUSCLE algorithm. The maximum likelihood tree shows the percent of 100 bootstrap analyses clustering at each node. The red text for each protein shows the length of coverage in BLAST hit followed by the percent identity relative to LRP1. Blue text is based on OMIM-annotated diseases for each gene. (B) Expression matrix for the genes of panel A using 200 data sets of tissues, cell lines, and single-cell annotations of the Human Protein Atlas. Correlations were calculated as 1 – Pearson's correlation. Below are the top samples for z-scores of LRP1, NID1, or NID2 expression levels.

Figure 2.

Patient morphology and time line. Facial (A) and hand (B) morphology of the proband. (C) Time line of both probands, including the genomics identified in blue. (DOL) Day of life.

Figure 3.

LRP1 variant characterization. Amino acid conservation from 194 LRP1 protein sequences (A) or codon selection scores from 124 open reading frame sequences of LRP1 (B). Each is shown as a sliding window of additive conservation of 21 amino acids/codons, and the two variants from patients are marked with a red line. (C) Protein models for Cys3807 and Val4136 (red). (D) Sequence alignments of LRP1 and LRP1B for amino acids around 3807 and 4136 (red). The 194 protein sequences were determined for conservation of each site (1 to 9, with 9 being >90% conserved), and 237 sequences of LRP1B were used to determine conservation with LRP1 (0 being not conserved with LRP1 and 1 to 9 based on conservation, with 9 being >90% conserved). Cysteines involved in disulfide bonds and conserved are highlighted in yellow, and other amino acids conserved with LRP1B are highlighted in gray.

Figure 4.

ENU(N-ethyl-N-nitrosourea) mutation in Lrp1 results in craniofacial abnormalities in mice. (A,B) A perinatal recessive ENU screen for novel genes involved craniofacial defects identified a mutant line with a c.Thr1019Cys transition in Lrp1 resulting in an p.F340S amino acid change, which disrupts the conserved YWTD motif in the extracellular domain. (C,D) Gross morphology of the ENU mutant, showing an abnormal head shape and short snout (arrow), smaller size, hemorrhage, and body wall abnormalities. (E,F) Coronal sections of E18.5 mutant and control heads showing cleft secondary palate in mutants. Arrowheads indicate unelevated palate shelves. (G,H) Alizarin red/alcian blue staining showing overall abnormal skull shape and markedly short mandible (arrow).

Figure 5.

Mouse phenotypes for Lrp1 alterations. (A) Embryo imaging of wild-type or Lrp1 homozygous knockout, with blue representing the LacZ replacement of Lrp1. Data is from the International Mouse Phenotyping Consortium (IMPC; www.mousephenotype.org/data/genes/MGI:96828). (B,C) Heterozygous Lrp1 knockout causing significant differences in male and female heart weight (B) and lens morphology (C). (D) All phenotypes observed within the Mouse Genome Informatics (MGI) database (Supplemental Table S1) fit within the summary terms for the modified mouse strains. (E) Skeleton images of Col2a1 conditional Lrp1-knockout with zoomed images of wild type (red) and homozygous (blue) animals.

Figure 6.

STRING analysis of the top correlating genes based on expression with LRP1. Correlated genes were identified from either human tissue analysis or single-cell analysis. Lines represent known connections from text mining or experimental interactions. The colors of the nodes are based on the phenotypes listed at the bottom, with false discovery rate (FDR) values listed.