Genome-wide expression analysis in fibroblast cell lines from probands with Pallister Killian syndrome

Abstract

Pallister Killian syndrome (OMIM: # 601803) is a rare multisystem disorder typically caused by tissue limited mosaic tetrasomy of chromosome 12p (isochromosome 12p). The clinical manifestations of Pallister Killian syndrome are variable with the most common findings including craniofacial dysmorphia, hypotonia, cognitive impairment, hearing loss, skin pigmentary differences and epilepsy. Isochromosome 12p is identified primarily in skin fibroblast cultures and in chorionic villus and amniotic fluid cell samples and may be identified in blood lymphocytes during the neonatal and early childhood period. We performed genomic expression profiling correlated with interphase fluorescent in situ hybridization and single nucleotide polymorphism array quantification of degree of mosaicism in fibroblasts from 17 Caucasian probands with Pallister Killian syndrome and 9 healthy age, gender and ethnicity matched controls. We identified a characteristic profile of 354 (180 up- and 174 down-regulated) differentially expressed genes in Pallister Killian syndrome probands and supportive evidence for a Pallister Killian syndrome critical region on 12p13.31. The differentially expressed genes were enriched for developmentally important genes such as homeobox genes. Among the differentially expressed genes, we identified several genes whose misexpression may be associated with the clinical phenotype of Pallister Killian syndrome such as downregulation of ZFPM2, GATA6 and SOX9, and overexpression of IGFBP2.

Figure 1. Clinical features of PKS.

(A)–(D). Full face and profile views of the facial features in two unrelated children with PKS. (E)–(G). Swirly hypo- and hyperpigmentation of the skin in 3 children with PKS. (H)–(J). Broad first toes in 3 children with PKS.

Figure 2. Patient and control sample clustering.

Red squares/circles represent PKS patients and Green squares/circles represent control samples. (A) Unsupervised clustering of 26 samples using all genes. (B) Unsupervised clustering of 26 samples using genes located on 12p.(C) PCA result. Proportion of Variance % (PC1-24.818, p 0.001; PC2-17.814, p 0.022; PC3-0.022, p 0.772).

Figure 3. Gene expression levels in PKS.

a: Mosaic 12p expression level correlation: Average expression of 171 genes on 12p in patients and controls. Red bars are patients and Grey is controls. X-axis represents samples and Y-axis shows average expression of genes on 12p. b: Level of i12p mosaicism compared to 12p gene expression: average of 64 genes with expression higher than the 3rd quartile of global expression distribution, were correlated to mosaicism%. The blue line in the figure is the fitting line of linear regression. Red diamonds are the probands and green are the controls.

Figure 4. BOX plot of HOX gene clusters.

HOX A is down- and HOX B Cluster is up-regulated in PKS patients.

Figure 5. Ingenuity pathway analysis of dysregulated genes in PKS.

Green circles represent the genes down-regulated in PKS probands, and red circles represent the genes up-regulated in PKS probands.

Figure 6. Schematic illustration of disease mechanism of PKS.