James Bristow

Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome

Noonan syndrome is a developmental disorder characterized by short stature, facial dysmorphia, congenital heart defects and skeletal anomalies. Increased RAS-mitogen-activated protein kinase (MAPK) signaling due to PTPN11 and KRAS mutations causes 50% of cases of Noonan syndrome. Here, we report that 22 of 129 individuals with Noonan syndrome without PTPN11 or KRAS mutation have missense mutations in SOS1, which encodes a RAS-specific guanine nucleotide exchange factor. SOS1 mutations cluster at codons encoding residues implicated in the maintenance of SOS1 in its autoinhibited form. In addition, ectopic expression of two Noonan syndrome–associated mutants induces enhanced RAS and ERK activation. The phenotype associated with SOS1 defects lies within the Noonan syndrome spectrum but is distinctive, with a high prevalence of ectodermal abnormalities but generally normal development and linear growth. Our findings implicate gain-of-function mutations in a RAS guanine nucleotide exchange factor in disease for the first time and define a new mechanism by which upregulation of the RAS pathway can profoundly change human development.

ChIP-Seq identification of weakly conserved heart enhancers

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme noncoding-sequence conservation has successfully predicted enhancers that are active in many tissues but has failed to identify substantial numbers of heart-specific enhancers. Here, we used ChIP-Seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over 3,000 candidate heart enhancers genome wide. Compared to enhancers active in othertissues we studied at this time point, most candidate heart enhancers were less deeply conserved in vertebrate evolution. Nevertheless, transgenic mouse assays of 130 candidate regions revealed that most function reproducibly as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type.

Tenascin-x deficiency mimics ehlers-danlos syndrome in mice through alteration of collagen deposition

Tenascin-X is a large extracellular matrix protein of unknown function. Tenascin-X deficiency in humans is associated with Ehlers–Danlos syndrome, a generalized connective tissue disorder resulting from altered metabolism of the fibrillar collagens. Because TNXB is the first Ehlers–Danlos syndrome gene that does not encode a fibrillar collagen or collagen-modifying enzyme, we suggested that tenascin-X might regulate collagen synthesis or deposition. To test this hypothesis, we inactivated Tnxb in mice. Tnxb−/− mice showed progressive skin hyperextensibility, similar to individuals with Ehlers–Danlos syndrome. Biomechanical testing confirmed increased deformability and reduced tensile strength of their skin. The skin of Tnxb−/− mice was histologically normal, but its collagen content was significantly reduced. At the ultrastructural level, collagen fibrils of Tnxb−/− mice were of normal size and shape, but the density of fibrils in their skin was reduced, commensurate with the reduction in collagen content. Studies of cultured dermal fibroblasts showed that although synthesis of collagen I by Tnxb−/− and wildtype cells was similar, Tnxb−/− fibroblasts failed to deposit collagen I into cell-associated matrix. This study confirms a causative role for TNXB in human Ehlers–Danlos syndrome and suggests that tenascin-X is an essential regulator of collagen deposition by dermal fibroblasts.

The Ehlers-Danlos syndrome: on beyond collagens

The Ehlers-Danlos syndrome (EDS) is a clinically and genetically heterogeneous connective tissue disorder affecting as many as 1 in 5,000 individuals (1). EDS is characterized in its most common form by hyperextensibility of the skin, hypermobility of joints often resulting in dislocations, and tissue fragility exemplified by easy bruising, atrophic scars following superficial injury, and premature rupture of membranes during pregnancy. The recognition of frequent ultrastructural abnormalities of collagen fibrils in EDS patients led to the concept that EDS is a disorder of fibrillar collagen metabolism (2). Following the identification of specific mutations in the genes encoding collagen types I, III, and V, as well as several collagen processing enzymes, the EDS classification scheme was collapsed into six distinct clinical syndromes (3), emphasizing the molecular basis of each form (Table ​(Table11). Table 1 The Villefranche classification of EDS Heterogeneity between the several clinical syndromes both complicates the diagnosis of EDS and makes accurate diagnosis imperative. Ultimately, one would like to be able to establish a molecular diagnosis for each EDS patient. This is a laudable goal because it may allow improved genetic counseling through correlation of mutant genotypes with specific outcomes or complications. However, as outlined below, the molecular defects described to date are not sufficient to explain disease in many EDS patients, including those with the most common classical and hypermobility types. As a result, the search for EDS genes recently has expanded beyond the collagens and collagen-modifying genes. An understanding of the complete complement of genes and proteins involved in EDS and the precise mechanisms by which they cause disease may teach us much about normal collagenous matrix deposition and remodeling. These processes are of critical importance during development, wound healing, and aging.

Large-scale discovery of enhancers from human heart tissue

Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers. To generate an accurate genome-wide map of human heart enhancers, we used an epigenomic enhancer discovery approach and identified ∼6,200 candidate enhancer sequences directly from fetal and adult human heart tissue. Consistent with their predicted function, these elements were markedly enriched near genes implicated in heart development, function and disease. To further validate their in vivo enhancer activity, we tested 65 of these human sequences in a transgenic mouse enhancer assay and observed that 43 (66%) drove reproducible reporter gene expression in the heart. These results support the discovery of a genome-wide set of noncoding sequences highly enriched in human heart enhancers that is likely to facilitate downstream studies of the role of enhancers in development and pathological conditions of the heart.

One bacterial cell, one complete genome.

While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200–900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

The Airborne Metagenome in an Indoor Urban Environment

The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.

Genome-wide examination of myoblast cell cycle withdrawal during differentiation

Skeletal and cardiac myocytes cease division within weeks of birth. Although skeletal muscle retains limited capacity for regeneration through recruitment of satellite cells, resident populations of adult myocardial stem cells have not been identified. Because cell cycle withdrawal accompanies myocyte differentiation, we hypothesized that C2C12 cells, a mouse myoblast cell line previously used to characterize myocyte differentiation, also would provide a model for studying cell cycle withdrawal during differentiation. C2C12 cells were differentiated in culture medium containing horse serum and harvested at various time points to characterize the expression profiles of known cell cycle and myogenic regulatory factors by immunoblot analysis. BrdU incorporation decreased dramatically in confluent cultures 48 hr after addition of horse serum, as cells started to form myotubes. This finding was preceded by up‐regulation of MyoD, followed by myogenin, and activation of Bcl‐2. Cyclin D1 was expressed in proliferating cultures and became undetectable in cultures containing 40% fused myotubes, as levels of p21WAF1/Cip1 increased and α‐actin became detectable. Because C2C12 myoblasts withdraw from the cell cycle during myocyte differentiation following a course that recapitulates this process in vivo, we performed a genome‐wide screen to identify other gene products involved in this process. Using microarrays containing ∼10,000 minimally redundant mouse sequences that map to the UniGene database of the National Center for Biotechnology Information, we compared gene expression profiles between proliferating, differentiating, and differentiated C2C12 cells and verified candidate genes demonstrating differential expression by RT‐PCR. Cluster analysis of differentially expressed genes revealed groups of gene products involved in cell cycle withdrawal, muscle differentiation, and apoptosis. In addition, we identified several genes, including DDAH2 and Ly‐6A, whose expression specifically was up‐regulated during cell cycle withdrawal coincident with early myoblast differentiation. 2002 Wiley‐Liss, Inc.

Increased endothelial NOS in lambs with increased pulmonary blood flow and pulmonary hypertension.

Altered pulmonary vascular reactivity is a source of morbidity and mortality for children with congenital heart defects and increased pulmonary blood flow. Nitric oxide (NO) is an important mediator of pulmonary vascular reactivity. The objective of this study was to characterize potential early alterations in expression, localization, and activity of endothelial NO synthase (eNOS) induced by increased pulmonary blood flow and pulmonary hypertension. Utilizing aortopulmonary vascular graft placement in the fetal lamb, we have established a unique animal model of pulmonary hypertension that mimics congenital heart disease with increased pulmonary blood flow. Ten fetal lambs underwent in utero placement of an aortopulmonary vascular graft (shunt). RNase protection assays and Western blotting were performed on lung tissue prepared from 4-wk-old shunt lambs and age-matched controls. eNOS mRNA (2.4:1, P < 0.05) and protein (2. 08:1, P < 0.05) were increased in lungs of shunt lambs. In situ hybridization and immunohistochemistry revealed that the increase was confined to the endothelium of pulmonary arteries. eNOS protein (1.55:1, P < 0.05) and tissue cGMP concentrations (2.1:1, P < 0.05) were also increased in isolated fifth-generation pulmonary arteries of shunt lambs. In addition, total lung eNOS activity was increased (2.9:1, P < 0.05). Thus we report a previously undescribed, early upregulation of eNOS gene expression and activity in lambs with increased pulmonary blood flow and pulmonary hypertension.

Development of Pulmonary Arteriovenous Fistulae in Children After Cavopulmonary Shunt

BACKGROUND The cavopulmonary shunt procedure is now used for palliation of complex congenital heart lesions in infants. While pulmonary arteriovenous fistulae (PAVF) are a well-known complication of this surgery in older patients, no study of the prevalence of this condition in children and young infants has been reported. METHODS AND RESULTS We compared 29 patients with cavopulmonary shunts or total caval exclusion with 53 control subjects evaluated by contrast echocardiography at the University of California, San Francisco. The primary cardiac lesion, age at the time of surgery, type of right heart bypass procedure, provision of auxiliary pulmonary blood flow, and changes in oxygen saturation over time were compared. The prevalence of PAVF in children after cavopulmonary anastomosis is 60%, higher than previously reported. The prevalence is significantly higher in infants < 6 months old and in those with a heterotaxy syndrome. The provision of an additional source of pulsatile, pulmonary blood flow appears to have little effect on the development of PAVF. Patients who developed PAVF had arterial oxygen saturations at the time of discharge from surgery similar to those who did not develop them. Those with PAVF had significantly lower arterial and pulmonary venous oxygen saturations at follow-up as a result of their intrapulmonary shunt. CONCLUSIONS Contrast echocardiography provides a sensitive method for the detection of PAVF. While the origins, natural history, and ultimate clinical significance of PAVF in children after cavopulmonary anastomosis are unclear, surveillance by contrast echocardiography is indicated for all patients who have had this procedure because PAVF may cause significant intrapulmonary right-to-left shunting in some patients.