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In a search for mediators of the p53 tumor suppressor pathway, which induces pleiotropic and often antagonistic cellular responses, we identified the long noncoding RNA (lncRNA) NEAT1. NEAT1 is an essential architectural component of paraspeckle nuclear bodies, whose pathophysiological relevance remains unclear. Activation of p53, pharmacologically or by oncogene-induced replication stress, stimulated the formation of paraspeckles in mouse and human cells. Silencing Neat1 expression in mice, which prevents paraspeckle formation, sensitized preneoplastic cells to DNA-damage-induced cell death and impaired skin tumorigenesis. We provide mechanistic evidence that NEAT1 promotes ATR signaling in response to replication stress and is thereby engaged in a negative feedback loop that attenuates oncogene-dependent activation of p53. NEAT1 targeting in established human cancer cell lines induced synthetic lethality with genotoxic chemotherapeutics, including PARP inhibitors, and nongenotoxic activation of p53. This study establishes a key genetic link between NEAT1 paraspeckles, p53 biology and tumorigenesis and identifies NEAT1 as a promising target to enhance sensitivity of cancer cells to both chemotherapy and p53 reactivation therapy.

Neat1 is a non-protein-coding RNA that serves as an architectural component of the nuclear bodies known as paraspeckles. Although cell-based studies indicate that Neat1 is a crucial regulator of gene expression, its physiological relevance remains unclear. Here, we find that Neat1 knockout (KO) mice stochastically fail to become pregnant despite normal ovulation. Unilateral transplantation of wild-type ovaries or the administration of progesterone partially rescued the phenotype, suggesting that corpus luteum dysfunction and concomitant low progesterone were the primary causes of the decreased fertility. In contrast to the faint expression observed in most of the adult tissues, Neat1 was highly expressed in the corpus luteum, and the formation of luteal tissue was severely impaired in nearly half of the Neat1 KO mice. These observations suggest that Neat1 is essential for the formation of the corpus luteum and for the subsequent establishment of pregnancy under a suboptimal condition that has not yet been identified., (© 2014. Published by The Company of Biologists Ltd.)

Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. We developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis-regulatory sequence analysis. iRegulon implements a genome-wide ranking-and-recovery approach to detect enriched transcription factor motifs and their optimal sets of direct targets. We increase the accuracy of network inference by using very large motif collections of up to ten thousand position weight matrices collected from various species, and linking these to candidate human TFs via a motif2TF procedure. We validate iRegulon on gene sets derived from ENCODE ChIP-seq data with increasing levels of noise, and we compare iRegulon with existing motif discovery methods. Next, we use iRegulon on more challenging types of gene lists, including microRNA target sets, protein-protein interaction networks, and genetic perturbation data. In particular, we over-activate p53 in breast cancer cells, followed by RNA-seq and ChIP-seq, and could identify an extensive up-regulated network controlled directly by p53. Similarly we map a repressive network with no indication of direct p53 regulation but rather an indirect effect via E2F and NFY. Finally, we generalize our computational framework to include regulatory tracks such as ChIP-seq data and show how motif and track discovery can be combined to map functional regulatory interactions among co-expressed genes. iRegulon is available as a Cytoscape plugin from http://iregulon.aertslab.org.

Leber Congenital Amaurosis (LCA), the most severe inherited retinal dystrophy, is genetically heterogeneous, with 14 genes accounting for 70% of patients. Here, 91 LCA probands underwent LCA chip analysis and subsequent sequencing of 6 genes (CEP290, CRB1, RPE65, GUCY2D, AIPL1and CRX), revealing mutations in 69% of the cohort, with major involvement of CEP290 (30%). In addition, 11 patients with early-onset retinal dystrophy (EORD) and 13 patients with Senior-Loken syndrome (SLS), LCA-Joubert syndrome (LCA-JS) or cerebello-oculo-renal syndrome (CORS) were included. Exhaustive re-inspection of the overall phenotypes in our LCA cohort revealed novel insights mainly regarding the CEP290-related phenotype. The AHI1 gene was screened as a candidate modifier gene in three patients with the same CEP290 genotype but different neurological involvement. Interestingly, a heterozygous novel AHI1 mutation, p.Asn811Lys, was found in the most severely affected patient. Moreover, AHI1 screening in five other patients with CEP290-related disease and neurological involvement revealed a second novel missense variant, p.His758Pro, in one LCA patient with mild mental retardation and autism. These two AHI1 mutations might thus represent neurological modifiers of CEP290-related disease., (© 2010 Wiley-Liss, Inc.)

Objective: The objective of this study is to look for evidence based or scientific guidelines for selection of newborns with congenital cytomegalovirus (CMV) infection that might benefit from treatment with ganciclovir., Materials and Methods: A literature search was conducted involving the MEDLINE database and the Cochrane Collaboration Library. Abstracts were reviewed to select pertinent articles dealing with ganciclovir therapy in neonates. References from selected articles as well as from reviews were screened for additional relevant articles. In total, 13 case reports (16 patients in all), three descriptive uncontrolled studies (20 patients in all), two randomized dose-comparative studies (54 patients in all) and one randomized controlled study (42 patients) were identified., Observations: All reported patients presented with central nervous system manifestation of CMV infection. Only the randomized controlled study showed a reduction of hearing deterioration in the treated group. Published predictors of hearing loss in congenitally CMV infected children allow identification of candidates that might benefit from treatment. Studies so far are promising but of insufficient number to make evidence based recommendations about indications for treatment of congenital CMV. As such, studies are very difficult to conduct and treatment of infants at high risk of hearing loss may appear justified. There is scientific data to help clinicians in selecting a subgroup of infants that is at higher risk of hearing deterioration and therefore might benefit the most from ganciclovir therapy.

In 15 Belgian subjects with prelingual sensorineural hearing impairment, the connexin 26 (GJB2) gene and the connexin 30 (GJB6) gene were analyzed for the presence of the 35delG mutation and the delta(GJB6-D13S1830) deletion first described by del Castillo et al in 2002. Seven patients were found to be homozygous for the 35delG mutation; 7 were combined heterozygotes for the 35delG mutation and the GJB6 deletion. In 11 subjects, phenotype and genotype were correlated. Significant, transient progression, in the range of 1.7 to 2.7 dB/y, was only found in 2 patients in the first part of the second decade of life. Hearing impairment was otherwise stable, with mean thresholds of 75, 90, and 100 dB at 0.125, 0.25, and 0.5 kHz, respectively, and 100 dB or higher at 1 to 4 kHz. There was no significant difference in hearing impairment between the patients with the homozygous 35delG mutation in GJB2 and those who are heterozygous for both the 35delG mutation and the deletion encompassing part of GJB6.

The combined findings of abnormalities of the incus and stapes, absence of the oval window, absence of the stapedius muscle (with absent pyramidal eminence and tympanic sinus in most cases), and abnormalities of different parts of the inner ear (dysplastic cochlea, hypoplastic or dysplastic vestibule, and absent semicircular canals) are characteristic of the CHARGE association. Computed tomography and magnetic resonance imaging using 1-mm-thick contiguous slices proved useful in demonstrating the broad spectrum of temporal bone abnormalities in patients with the CHARGE association.

We present the clinical findings and follow-up data of four female children with Cohen syndrome, two sisters and one pair of dizygotic female twins. The most characteristic findings from birth on were as follows: 1. Low-normal growth parameters at birth. 2. Mild hypotonia and evidence of progressive microcephaly with narrow forehead in the first year of life. 3. Neutropenia was present from the beginning, remained unchanged over the years and is not associated with higher susceptibility to infections. 4. Autistic behavior and severe psychomotor retardation up to the age of 2 years. At that age the ocular anomalies with high-grade myopia and chorioretinal dystrophy were diagnosed. Correction of the myopia resulted in a marked catch-up in psychomotor development. 5. After the age of 6 years facial stigmata became more evident with short philtrum of the upper lip and broad and large upper incisors. 6. Tendency to truncular obesity with rest hypotonia and poor muscle development after the ages of 6 to 8 years. The clinical findings and follow-up data in the present four children with Cohen syndrome illustrate that the diagnosis of Cohen syndrome in infancy is very difficult.

A 3 1/2 year-old severely microcephalic male is reported with a paracentric inversion in the long arm of a chromosome 14. This is the second report of nonfamilial paracentric inversion in man.