Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms

Abstract

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.

Keywords: CdLS; Cornelia de Lange Syndrome; HDAC8; NIPBL; RAD21; SMC1A; SMC3; cohesin; genome; transcription.

Figure 1.

Overview of CdLS. A) Typical facial features in CdLS with the classic features seen in the two individuals on the left with NIPBL pathogenic variants and more subtle/milder manifestations in the two individuals on the right with HDAC8 and SMC1A pathogenic variants. B. Variable upper limb differences seen in CdLS ranging from severe oligodactyly on the left to small hands with single palmar creases and hypoplasia of the 5^th finger. C. Simplified representation of the cohesin complex and core structural and regulatory proteins involved in CdLS that disrupt cohesin’s non-canonical role in regulating developmental gene expression.

Figure 2.

A. Summary of all probands screened and distribution of causative variants and B. List of genes with causative variants and prevalence within this population.

Figure 3.

Schematic representation of pathogenic variants in A. NIPBL variants, B. SMC1A, C. HDAC8, D. SMC3, and E. RAD21 identified in this cohort.

Figure 4.

Recurrent pathogenic variants in CdLS genes and resultant phenotypes. A. List of recurrent variants found in the known CdLS genes, † variants affecting same amino residues. B. Phenotypic representations of a subset of probands listed in A with recurrent variants at the same amino acid residue. While most probands with recurrent variants had consistent phenotypic severities there were some exceptions (e.g., for the p.R2298C recurrent variants only 2/5 had severe limb reduction differences as seen in the proband on the right) indicating that while genotype is a strong driver of phenotype there are likely other genetic and environmental modifiers at play.

Figure 5.

NIPBL intragenic copy number variations (CNVs) in CdLS probands. A. List of NIPBL CNVs identified in this cohort with diagnostic certainty and severity scores. B. Phenotypic representation of a subset of these probands with characteristic but variable involvement of facial features and upper limbs.

Figure 6.

A. Novel and atypical genes identified to have causative variants in this CdLS cohort with B. representative photos of affected individuals.

Figure 7.

A. Protein-protein interactions amongst genes with identified variants. Core CdLS genes are indicated by diamond shapes, the prevalence of variants indicated by the size of shapes, and the strength of interactions between proteins indicated by the width of lines. B. HPO terms associated with mutated genes identified in this study. C. Gene ontologies by molecular function and biological processes.

Figure 8.

Chromosomal position and boundaries of rare CNVs not encompassing known CdLS Loci. A. Chromosomal coordinate and phenotypes of 15 probands with CNVs. B. Representative facial features of 6 of these probands.

Figure 9.

Genotype-phenotype correlations in CdLS and related diagnoses. The genetic contributors to the various phenotypic subclassifications of CdLS include a predominance of NIPBL truncating variants contributing to the “classic/severe” CdLS phenotype with rare NIPBL missense variants in critical domains as well as possible other mutational mechanisms/novel genes contributing to the small percent classic/severe CdLS probands in which a mutation has not been identified. The moderate phenotype is caused predominantly by missense and more terminal truncating variants in NIPBL as well as by variants in most of the other cohesin-related CdLS genes (SMC1A, SMC3, HDAC8, RAD21) with some variants in non-cohesin related genes and additional mechanisms/genes still to be identified. The mild CdLS phenotype demonstrates a similar distribution with a greater representation of non-NIPBL-related variants. The “atypical” phenotypes are primarily caused by variants in non-cohesin related genes, however, there is a smaller contribution of cohesin gene mutation as well (e.g. truncating variants in SMC1A, HDAC8, RAD21, and the STAG genes).