CRIM1 haploinsufficiency causes defects in eye development in human and mouse

Abstract

Colobomatous macrophthalmia with microcornea syndrome (MACOM, Online Mendelian Inheritance in Man (OMIM) 602499) is an autosomal dominantly inherited malformation of the eye, which is characterized by microcornea with increased axial length, coloboma of the iris and of the optic disc, and severe myopia. We performed whole-exome sequencing (WES) in two affected individuals from the 2p23-p16-linked MACOM family, which includes 13 affected individuals in 3 generations. As no shared novel variation was found on the linked haplotype, we performed copy number variation (CNV) analysis by comparing the coverage of all exons in the WES data sets of the 2 patients with the coverage of 26 control exomes. We identified a heterozygous deletion predicted to span 22 kb including exons 14-17 of CRIM1 (cysteine-rich transmembrane bone morphogenetic protein (BMP) regulator 1). Quantitative PCR (qPCR) analysis confirmed the deletion, which was present in 11 affected individuals. Split-read analysis of WES data followed by breakpoint PCR and Sanger sequencing determined both breakpoints flanked by a 4-bp microhomology (CTTG). In the mouse, Crim1 is a growth-factor-binding protein with pleiotropic roles in the development of multiple organs, including the eye. To investigate the role of Crim1 during eye development in mice, we crossed a Crim1(flox) mouse line with the Ap2α-cre mouse line, which expresses Cre in the head surface ectoderm. Strikingly, we observed alterations of eye development in homozygous mice leading to severe anatomical and morphological changes overlapping with the anomalies observed in MACOM patients. Taken together, these findings identify CRIM1 as the causative gene for MACOM syndrome and emphasize the importance of CRIM1 in eye development.

High‐throughput custom capture sequencing identifies novel mutations in coloboma‐associated genes: Mutation in DNA‐binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma

“…Phenotypic variability in ocular conditions likely depends on multiple factors, including genetic variation in coding and noncoding elements in and around genes important for orchestrating ocular development (Azuma et al, ; Chang et al, ; George et al, ; Reis & Semina, ; Sanyanusin et al, ). Mutations leading to partial or complete loss of gene function have been shown to cause severe ocular and nonocular systemic manifestations in addition to coloboma (Asai‐Coakwell et al, ; Beleggia et al, ; C. Liu et al, ; Reis & Semina, ; Ye et al, ). Genes that encode transcriptional regulators (e.g., PAX2 , PAX6 , MITF , TFAP2A , and CHD7 ), members of secreted signaling pathways, such as transforming growth factor‐beta/bone morphogenetic protein (TGFB/BMP) signaling ( BMP7 , GDF3 , and GDF6 ), Hippo signaling ( YAP1 ), retinoic acid (RA) signaling ( ALDH1A3 , STRA6 , and RARB ) and those involved in membrane transport ( ABCB6 ) have been implicated in causing coloboma when mutated in humans (Reis & Semina, ).…”

“…Phenotypic variability in ocular conditions likely depends on multiple factors, including genetic variation in coding and noncoding elements in and around genes important for orchestrating ocular development (Azuma et al, 2003;Chang et al, 2006;George et al, 2016;Reis & Semina, 2015;Sanyanusin et al, 1995). Mutations leading to partial or complete loss of gene function have been shown to cause severe ocular and nonocular systemic manifestations in addition to coloboma (Asai-Coakwell et al, 2009;Beleggia et al, 2015;C. Liu et al, 2016;Reis & Semina, 2015;Ye et al, 2010).…”

EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model

“…For cases without causal variants in the most common MAC genes, whole exome sequencing represents an efficient method of screening numerous known ocular genes along with the entire exome to identify the causative variant (Need et al, ; Reis et al, ; Deml et al, ; Weh et al, ). The whole exome sequencing approach has demonstrated success in discovering novel causative genes in MAC conditions as well (Zahrani et al, ; Kelberman et al, ; Williamson et al, ; Beleggia et al, ; Deml et al, ). Interpretation of whole exome sequencing results is often challenging due to the large number of identified variants.…”

A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies

“…Thus, it seems that ongoing reduction in costs as well as improvements in sensitivity and specificity will make NGS the technique of choice for IRD diagnoses in the near future. In fact, NGS, including whole-exome sequencing (WES) analysis, has been successfully used recently for the molecular diagnosis of retinal dystrophies [6,7,8,9,10,11,12]. However, although WES/whole-genome sequencing (WGS) approaches are increasingly used in clinical medicine, questions are being raised about the interpretation and reporting of clinical findings [8].…”

“…In fact, NGS, including whole-exome sequencing (WES) analysis, has been successfully used recently for the molecular diagnosis of retinal dystrophies [6,7,8,9,10,11,12]. However, although WES/whole-genome sequencing (WGS) approaches are increasingly used in clinical medicine, questions are being raised about the interpretation and reporting of clinical findings [8]. One of the current limiting factors is the huge amount of data generated, which makes NGS highly time-consuming and requires the participation of specialized technicians and bioinformaticians, especially in projects using WES/WGS, which are still rather expensive options for studies involving large cohorts.…”