Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum.

Background: Oculoauriculovertebral Spectrum (OAVS) encompasses a wide variety of anomalies on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular and vertebral anomalies. We present the genetic findings of a large three-generation family with multiple members affected with macrostomia, preauricular tags and uni- or bilateral ptosis following an autosomal dominant segregation pattern. Methods: We generated whole genome sequencing data for the proband, affected parent and unaffected paternal grandparent followed by Sanger sequencing on 23 family members for the top 10 candidate genes: KCND2, PDGFRA, CASP9, NCOA3, WNT10A, SIX1, MTF1, KDR/VEGFR2, LRRK1, and TRIM2. We performed parent and sibling-based transmission disequilibrium tests and burden analysis to explore segregation and burden of candidate gene mutations. Bioinformatic analyses investigated the biological connection between genes and the abnormal phenotypes. Results: Overall, rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best evidence of segregation with the OAV phenotypes in this family. When considering affection with any of the 3 OAVS phenotypes as an outcome, parent-TDTs and sib-TDTs (unadjusted p-values) found that SIX1 (p=0.025, p=0.052), followed by PDGFRA (p=0.180, p=0.069) and KDR/VEGFR2 (p=0.180, p=0.069) have the strongest associations in this family. Burden analysis via a penalized linear mixed model identified SIX1 (RC=0.87) and PDGFRA (RC=0.98) as having the strongest association with OAVS severity. Using phenotype-specific ogfrautcomes, sib-TDTs identified associations between (1) SIX1 with uni- or bilateral ptosis (p=0.049) and ear tags (p=0.01), (2) PDGFRA and KDR/VEGFR2 with ear tags (both p<0.01). Conclusion: Our study reports the genomic findings of a large family with multiple individuals affected with OAVS phenotypes with autosomal dominant inheritance. Our findings narrow down to three potential candidate genes, SIX1, PDGFRA, and KDR/VEGFR2. Among these, SIX1 has been previously associated with OAVS ear malformations and it is co-expressed with EYA1 during ear development. Attempts to strengthen the genotype-phenotype co-relation underlying the OAVS of phenotypes are essential to discover the etiological factors leading to this complex and burdensome condition as well as for family counseling and prevention efforts.

Radiomic biomarkers informative of cancerous transformation in neurofibromatosis-1 plexiform tumors.

BACKGROUND: This study explores whether objective, quantitative radiomic biomarkers derived from magnetic resonance (MR), positron emission tomography (PET), and computed tomography (CT) may be useful in reliably distinguishing malignant peripheral nerve sheath tumors (MPNST) from benign plexiform neurofibromas (PN). METHODS: A registration and segmentation pipeline was established using a cohort of NF1 patients with histopathological diagnosis of PN or MPNST, and medical imaging of the PN including MR and PET-CT. The corrected MR datasets were registered to the corresponding PET-CT via landmark-based registration. PET standard-uptake value (SUV) thresholds were used to guide segmentation of volumes of interest: MPNST-associated PET-hot regions (SUV≥3.5) and PN-associated PET-elevated regions (2.0

Screening of Living Kidney Donors for Genetic Diseases Using a Comprehensive Genetic Testing Strategy.

Related living kidney donors (LKDs) are at higher risk of end-stage renal disease (ESRD) compared with unrelated LKDs. A genetic panel was developed to screen 115 genes associated with renal diseases. We used this panel to screen six negative controls, four transplant candidates with presumed genetic renal disease and six related LKDs. After removing common variants, pathogenicity was predicted using six algorithms to score genetic variants based on conservation and function. All variants were evaluated in the context of patient phenotype and clinical data. We identified causal variants in three of the four transplant candidates. Two patients with a family history of autosomal dominant polycystic kidney disease segregated variants in PKD1. These findings excluded genetic risk in three of four relatives accepted as potential LKDs. A third patient with an atypical history for Alport syndrome had a splice site mutation in COL4A5. This pathogenic variant was excluded in a sibling accepted as an LKD. In another patient with a strong family history of ESRD, a negative genetic screen combined with negative comparative genomic hybridization in the recipient facilitated counseling of the related donor. This genetic renal disease panel will allow rapid, efficient and cost-effective evaluation of related LKDs.

Disruption of the non-canonical Wnt gene PRICKLE2 leads to autism-like behaviors with evidence for hippocampal synaptic dysfunction.

Autism spectrum disorders (ASDs) have been suggested to arise from abnormalities in the canonical and non-canonical Wnt signaling pathways. However, a direct connection between a human variant in a Wnt pathway gene and ASD-relevant brain pathology has not been established. Prickle2 (Pk2) is a post-synaptic non-canonical Wnt signaling protein shown to interact with post-synaptic density 95 (PSD-95). Here, we show that mice with disruption in Prickle2 display behavioral abnormalities including altered social interaction, learning abnormalities and behavioral inflexibility. Prickle2 disruption in mouse hippocampal neurons led to reductions in dendrite branching, synapse number and PSD size. Consistent with these findings, Prickle2 null neurons show decreased frequency and size of spontaneous miniature synaptic currents. These behavioral and physiological abnormalities in Prickle2 disrupted mice are consistent with ASD-like phenotypes present in other mouse models of ASDs. In 384 individuals with autism, we identified two with distinct, heterozygous, rare, non-synonymous PRICKLE2 variants (p.E8Q and p.V153I) that were shared by their affected siblings and inherited paternally. Unlike wild-type PRICKLE2, the PRICKLE2 variants found in ASD patients exhibit deficits in morphological and electrophysiological assays. These data suggest that these PRICKLE2 variants cause a critical loss of PRICKLE2 function. The data presented here provide new insight into the biological roles of Prickle2, its behavioral importance, and suggest disruptions in non-canonical Wnt genes such as PRICKLE2 may contribute to synaptic abnormalities underlying ASDs.

Methylation of the p16(INK4a) promoter region in telomerase immortalized human keratinocytes co-cultured with feeder cells.

Human keratinocytes grown in co-culture with fibroblast feeder cells have an extended in vitro lifespan and delayed accumulation of the tumor suppressor protein p16(INK4a) when compared to the same cells grown on tissue culture plastic alone. Previous studies have indicated that human keratinocytes can be immortalized by telomerase activity alone when grown in co-culture with feeder cells, suggesting that loss of the p16(INK4a)/Rb pathway is not required for immortalization. Using two independent human keratinocyte cell strains, we found that exogenous telomerase expression and co-culture with feeder cells results in efficient extension of lifespan without an apparent crisis. However, when these cells were transferred from the co-culture environment to plastic alone they experienced only a brief period of slowed growth before continuing to proliferate indefinitely. Examination of immortal cell lines demonstrated p16(INK4a) promoter methylation had occurred in both the absence and presence of feeder cells. Reintroduction of p16(INK4a) into immortal cell lines resulted in rapid growth arrest. Our results suggest that p16(INK4a)/Rb-induced telomere-independent senescence, although delayed in the presence of feeders, still provides a proliferation barrier to human keratinocytes in this culture system and that extended culture of telomerase-transduced keratinocytes on feeders can lead to the methylation of p16(INK4a).