TGFBR1 mutations associated with Loeys-Dietz syndrome are inactivating

To assess the effect of Loeys-Dietz syndrome (LDS) mutations affecting TGFΒR1 a selection of seven disease-associated amino acid substitutions were introduced into wild type TGFβR1 and constitutively active TGFβR1^T204D. Receptor function was tested by co-transfection with a luciferase reporter or EGFP-tagged SMAD2 in HEK293 cells. All of the mutations were found to be inactivating for canonical TGF-β signaling. Differences in residual activity were not found to correlate with disease subtype. In co-transfection experiments with equal amounts wild-type receptor, the LDS mutations were found to confer a modest dominant negative effect. These results are discussed in relation to LDS and the related Marfan syndrome.     

TGFBR1 mutations associated with Loeys-Dietz syndrome are inactivating

To assess the effect of Loeys-Dietz syndrome (LDS) mutations affecting TGFΒR1 a selection of seven disease-associated amino acid substitutions were introduced into wild type TGFβR1 and constitutively active TGFβR1(T204D). Receptor function was tested by co-transfection with a luciferase reporter or EGFP-tagged SMAD2 in HEK293 cells. All of the mutations were found to be inactivating for canonical TGF-β signaling. Differences in residual activity were not found to correlate with disease subtype. In co-transfection experiments with equal amounts wild-type receptor, the LDS mutations were found to confer a modest dominant negative effect. These results are discussed in relation to LDS and the related Marfan syndrome.     

RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome

Tylosis esophageal cancer (TOC) is an autosomal-dominant syndrome characterized by palmoplantar keratoderma, oral precursor lesions, and a high lifetime risk of esophageal cancer. We have previously localized the TOC locus to a small genomic interval within chromosomal region 17q25. Using a targeted capture array and next-generation sequencing, we have now identified missense mutations (c.557T>C [p.Ile186Thr] and c.566C>T [p.Pro189Leu] in RHBDF2, which encodes the inactive rhomboid protease RHBDF2 (also known as iRhom2), as the underlying cause of TOC. We show that the distribution of RHBDF2 in tylotic skin is altered in comparison with that in normal skin, and immortalized tylotic keratinocytes have decreased levels of total epidermal growth factor receptor (EGFR) and display an increased proliferative and migratory potential relative to normal cells, even when normal cells are stimulated with exogenous epidermal growth factor. It would thus appear that EGFR signaling is dysregulated in tylotic cells. Furthermore, we also show an altered localization of RHBDF2 in both tylotic and sporadic squamous esophageal tumors. The elucidation of a role of RHBDF2 in growth-factor signaling in esophageal cancer will help to determine whether targeting this pathway in chemotherapy for this and other squamous cell carcinomas will be effective.     

Germline missense mutations affecting KRAS Isoform B are associated with a severe Noonan syndrome phenotype

Noonan syndrome (NS) is a developmental disorder characterized by short stature, facial dysmorphia, congenital heart disease, and multiple skeletal and hematologic defects. NS is an autosomal dominant trait and is genetically heterogeneous. Gain of function of SHP-2, a protein tyrosine phosphatase that positively modulates RAS signaling, is observed in nearly 50% of affected individuals. Here, we report the identification of heterozygous KRAS gene mutations in two subjects exhibiting a severe NS phenotype with features overlapping those of cardiofaciocutaneous and Costello syndromes. Both mutations were de novo and affected exon 6, which encodes the C-terminal portion of KRAS isoform B but does not contribute to KRAS isoform A. Structural analysis indicated that both substitutions (Val152Gly and Asp153Val) perturb the conformation of the guanine ring-binding pocket of the protein, predicting an increase in the guanine diphosphate/guanine triphosphate (GTP) dissociation rate that would favor GTP binding to the KRASB isoform and bypass the requirement for a guanine nucleotide exchange factor.     

Oestrogen deficiency and growth hormone treatment in childhood are not associated with hearing in adults with turner syndrome

BACKGROUND/AIMS: Women with Turner syndrome (TS) have an increased prevalence of hearing loss, with conductive (CHL) and sensorineural (SNHL) components. The association between hearing loss and clinical parameters, particularly oestrogen and previous growth hormone (GH) treatment, was investigated. METHODS: A cross-sectional study of pure tone audiometry tests in an adult TS population. Previous ENT history, karyotype, anthropomorphic measurements and the impact of oestrogen and childhood GH therapy were assessed. One hundred and thirty-eight women (median age 29, range 16-67 years) completed the study. RESULTS: Normal hearing was found in 20.3% of women, CHL in 18.8%, SNHL in 57.2% and confounding factors in 3.6%. Neither CHL nor SNHL were associated with oestrogen deficiency or GH treatment independent of age. CHL but not SNHL was more common in those with a history of recurrent otitis media (p < 0.01) and monosomy 45,X (p < 0.01). CONCLUSIONS: Current regimens of oestrogen and GH therapy have no impact on adult hearing loss in TS, independent of age. The prevalence of SNHL increases with age. CHL but not SNHL is associated with ENT history and karyotype. According to present evidence, the only possible intervention to reduce hearing loss in women with TS remains assiduous treatment of ENT problems in childhood.     

Serum histidine-rich glycoprotein levels are decreased in acquired immune deficiency syndrome and by steroid therapy

Using radial immunodiffusion serum histidine-rich glycoprotein (HRG) levels were measured in acquired immune deficiency syndrome (AIDS) patients, in end-stage renal disease (ESRD) patients after renal transplantation and immunosuppressive steroid therapy, and in asthma and chronic obstructive pulmonary disease (COPD) patients treated with steroids. Compared with controls (12.5 +/- 3.0 mg/dl), HRG levels were significantly decreased in patients with AIDS (5.7 +/- 1.8 mg/dl, P less than 0.005): in patients with ESRD after renal transplantation with steroid therapy (4.4 +/- 1.1 mg/dl, P less than 0.005); and in asthmatic and COPD patients receiving steroids in acute (7.6 +/- 2.9 mg/dl, P less than 0.005) or chronic (7.4 +/- 3.0 mg/dl, P less than 0.025) high-dose regimens. In contrast, levels of hemopexin, another serum glycoprotein synthesized by the liver, were not lowered in these patients. These results show that serum HRG levels are selectively decreased in AIDS and in patients treated with immunosuppressive steroids.     

Goldenhar syndrome associated with growth hormone deficiency

Goldenhar syndrome is a rare disorder of unknown etiology. The most frequent findings are vertebral defects, hemifacial microsomia and ear abnormalities. We present an 8-year-old boy with oculo-auriculo-vertebral (Goldenhar) syndrome. He also had a parachute mitral valve and growth hormone deficiency. Parachute mitral valve is a previously unreported finding while growth hormone deficiency was reported just in one case in the literature.     

Functional chromatin features are associated with structural mutations in cancer

Background

Structural mutations (SMs) play a major role in cancer development. In some cancers, such as breast and ovarian, DNA double-strand breaks (DSBs) occur more frequently in transcribed regions, while in other cancer types such as prostate, there is a consistent depletion of breakpoints in transcribed regions. Despite such regularity, little is understood about the mechanisms driving these effects. A few works have suggested that protein binding may be relevant, e.g. in studies of androgen receptor binding and active chromatin in specific cell types. We hypothesized that this behavior might be general, i.e. that correlation between protein-DNA binding (and open chromatin) and breakpoint locations is common across divergent cancers.

Results

We investigated this hypothesis by comprehensively analyzing the relationship among 457 ENCODE protein binding ChIP-seq experiments, 125 DnaseI and 24 FAIRE experiments, and 14,600 SMs from 8 diverse cancer datasets covering 147 samples. In most cancers, including breast and ovarian, we found enrichment of protein binding and open chromatin in the vicinity of SM breakpoints at distances up to 200 kb. Furthermore, for all cancer types we observed an enhanced enrichment in regions distant from genes when compared to regions proximal to genes, suggesting that the SM-induction mechanism is independent from the bias of DSBs to occur near transcribed regions. We also observed a stronger effect for sites with more than one protein bound.

Conclusions

Protein binding and open chromatin state are associated with nearby SM breakpoints in many cancer datasets. These observations suggest a consistent mechanism underlying SM locations across different cancers.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1013) contains supplementary material, which is available to authorized users.     

Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome

It is not understood how immune inflammation influences the pathogenesis of severe acute respiratory syndrome (SARS). One area of strong controversy is the role of interferon (IFN) responses in the natural history of SARS. The fact that the majority of SARS patients recover after relatively moderate illness suggests that the prevailing notion of deficient type I IFN-mediated immunity, with hypercytokinemia driving a poor clinical course, is oversimplified. We used proteomic and genomic technology to systematically analyze host innate and adaptive immune responses of 40 clinically well-described patients with SARS during discrete phases of illness from the onset of symptoms to discharge or a fatal outcome. A novel signature of high IFN-alpha, IFN-gamma, and IFN-stimulated chemokine levels, plus robust antiviral IFN-stimulated gene (ISG) expression, accompanied early SARS sequelae. As acute illness progressed, SARS patients entered a crisis phase linked to oxygen saturation profiles. The majority of SARS patients resolved IFN responses at crisis and expressed adaptive immune genes. In contrast, patients with poor outcomes showed deviated ISG and immunoglobulin gene expression levels, persistent chemokine levels, and deficient anti-SARS spike antibody production. We contend that unregulated IFN responses during acute-phase SARS may culminate in a malfunction of the switch from innate immunity to adaptive immunity. The potential for the use of the gene signatures we describe in this study to better assess the immunopathology and clinical management of severe viral infections, such as SARS and avian influenza (H5N1), is therefore worth careful examination.     

Post-streptococcal antibodies are associated with metabolic syndrome in a population-based cohort

Background

Streptococcal infections are known to trigger autoimmune disorders, affecting millions worldwide. Recently, we found an association between post-streptococcal autoantibodies against Protein Disulphide Isomerase (PDI), an enzyme involved in insulin degradation and insulin resistance. This led us to evaluate associations between post-streptococcal antibodies and metabolic syndrome, as defined by the updated National Cholesterol Education Program definition, 2005.

Methods and Findings

Metabolic data (HDL, triglycerides, fasting glucose, blood pressure, waist circumference, BMI, smoking), post-streptococcal antibodies (anti-Streptolysin O (ASO) and anti-PDI), and C-reactive protein (CRP, as a general inflammatory marker), were assessed in 1156 participants of the Wisconsin Sleep Cohort Study. Anti-PDI antibodies were found in 308 participants (26.6%), ASO≥100 in 258 (22.3%), and 482 (41.7%) met diagnostic criteria for metabolic syndrome. Anti-PDI antibodies but not ASO were significantly associated with metabolic syndrome [n = 1156, OR 1.463 (95% CI 1.114, 1.920), p = 0.0062; adjusted for age, gender, education, smoking]. Importantly, the anti-PDI - metabolic syndrome association remained significant after adjusting for CRP and fasting insulin.

Conclusions

Post-streptococcal anti-PDI antibodies are associated with metabolic syndrome regardless of fasting insulin and CRP levels. Whereas these data are in line with a growing body of evidence linking infections, immunity and metabolism, additional studies are necessary to establish the post-streptococcal – metabolic syndrome association.     

Deleterious mutations are characterized by higher genomic heterozygosity than other genic variants in plant genomes

Deleterious mutations can reduce the fitness of crop varieties, which limits the plant breeding efficacy. While crop deleterious mutations have been extensively examined, most studies focused on one specific crop with different analyzing methods, which hinders unveiling shared genomic characteristics of deleterious mutations across diverse crops. Here we used standardized approaches to characterize the deleterious mutations in genomes of domesticated inbreeding (i.e., rice, soybean, and tomato) and clonally propagated crops (i.e., grape and pineapple). We found that deleterious mutations are commonly targeted by purifying selection, and are over-presented in a nearly fixed derived allele frequency in the course of plant domestication. Further, a generally negative correlation between genetic load and the artificial selection strength is observed. Importantly, we consistently uncovered the higher derived genomic heterozygosity for deleterious mutations compared to other genic variants. This study broadens our understanding of the evolution of deleterious mutations in plant genomes.     

Germline mutations in the Wilms' tumor suppressor gene are associated with abnormal urogenital development in Denys-Drash syndrome.

Denys-Drash syndrome is a rare human condition in which severe urogenital aberrations result in renal failure, pseudohermaphroditism, and Wilms' tumor (nephroblastoma). To investigate its possible role, we have analyzed the coding exons of the Wilms' tumor suppressor gene (WT1) for germline mutations. In ten independent cases of Denys-Drash syndrome, point mutations in the zinc finger domains of one WT1 gene copy were found. Nine of these mutations are found within exon 9 (zinc finger III); the remaining mutation is in exon 8 (zinc finger II). These mutations directly affect DNA sequence recognition. In two families analyzed, the mutations were shown to arise de novo. Wilms' tumors from three individuals and one juvenile granulosa cell tumor demonstrate reduction to homozygosity for the mutated WT1 allele. Our results provide evidence of a direct role for WT1 in Denys-Drash syndrome and thus urogenital system development.