The Royal Children's Hospital Foundation

Prediction of gene regulatory sequences using phylogenetic footprinting has advanced considerably but lacks experimental validation. Here, we report whether transcription factor binding sites predicted by dot plotting or web-based Trafac analysis could be validated by chromatin immunoprecipitation assays. MYC overexpression enhances glycolysis without hypoxia and hence may contribute to altered tumor metabolism. Because the full spectrum of glycolytic genes directly regulated by Myc is not known, we chose Myc as a model transcription factor to determine whether it binds target glycolytic genes that have conserved canonical Myc binding sites or E boxes (5'-CACGTG-3'). Conserved canonical E boxes in ENO1, HK2, and LDHA occur in 31- to 111-bp islands with high interspecies sequence identity (>65%). Trafac analysis revealed another region in ENO1 that corresponds to a murine region with a noncanonical E box. Myc bound all these conserved regions well in the human P493-6 B lymphocytes. We also determined whether Myc could bind nonconserved canonical E boxes found in the remaining human glycolytic genes. Myc bound PFKM, but it did not significantly bind GPI, PGK1, and PKM2. Binding to BPGM, PGAM2, and PKLR was not detected. Both GAPD and TPI1 do not have conserved E boxes but are induced and bound by Myc through regions with noncanonical E boxes. Our results indicate that Myc binds well to conserved canonical E boxes, but not nonconserved E boxes. However, the binding of Myc to unpredicted genomic regions with noncanonical E boxes reveals a limitation of phylogenetic footprinting. In aggregate, these observations indicate that Myc is an important regulator of glycolytic genes, suggesting that MYC plays a key role in a switch to glycolytic metabolism during cell proliferation or tumorigenesis.

The T-box family transcription factor gene TBX20 acts in a conserved regulatory network, guiding heart formation and patterning in diverse species. Mouse Tbx20 is expressed in cardiac progenitor cells, differentiating cardiomyocytes, and developing valvular tissue, and its deletion or RNA interference-mediated knockdown is catastrophic for heart development. TBX20 interacts physically, functionally, and genetically with other cardiac transcription factors, including NKX2- 5, GATA4, and TBX5, mutations of which cause congenital heart disease (CHD). Here, we report nonsense (Q195X) and missense (I152M) germline mutations within the T-box DNA-binding domain of human TBX20 that were associated with a family history of CHD and a complex spectrum of developmental anomalies, including defects in septation, chamber growth, and valvulogenesis. Biophysical characterization of wild-type and mutant proteins indicated how the missense mutation disrupts the structure and function of the TBX20 T-box. Dilated cardiomyopathy was a feature of the TBX20 mutant phenotype in humans and mice, suggesting that mutations in developmental transcription factors can provide a sensitized template for adult-onset heart disease. Our findings are the first to link TBX20 mutations to human pathology. They provide insights into how mutation of different genes in an interactive regulatory circuit lead to diverse clinical phenotypes, with implications for diagnosis, genetic screening, and patient follow-up.

Adult hematopoietic stem cells (HSCs) exist in a relatively quiescent state in the bone marrow (BM) microenvironment to fulfill long-term self-renewal and multilineage differentiation functions, an event that is tightly regulated by extrinsic and intrinsic cues. However, the mechanism coordinating the quiescent state of HSCs and their retention in the BM microenvironment remains poorly understood. In a conditional-knockout mouse model, we show that Cdc42(-/-) HSCs enter the active cell cycle, resulting in significantly increased number and frequency of the stem/progenitor cells in the BM. Cdc42 deficiency also causes impaired adhesion, homing, lodging, and retention of HSCs, leading to massive egress of HSCs from BM to distal organs and peripheral blood and to an engraftment failure. These effects are intrinsic to the HSCs and are associated with deregulated c-Myc, p21(Cip1), beta1-integrin, and N-cadherin expressions and defective actin organization. Thus, Cdc42 is a critical coordinator of HSC quiescence maintenance and interaction with the BM niche.

Optic nerve assessment is important for many blinding diseases, with cup-to-disc ratio (CDR) assessments commonly used in both diagnosis and progression monitoring of glaucoma patients. Optic disc, cup, rim area and CDR measurements all show substantial variation between human populations and high heritability estimates within populations. To identify loci underlying these quantitative traits, we performed a genome-wide association study in two Australian twin cohorts and identified rs3858145, P=6.2x10(-10), near the ATOH7 gene as associated with the mean disc area. ATOH7 is known from studies in model organisms to play a key role in retinal ganglion cell formation. The association with rs3858145 was replicated in a cohort of UK twins, with a meta-analysis of the combined data yielding P=3.4x10(-10). Imputation further increased the evidence for association for several SNPs in and around ATOH7 (P=1.3x10(-10) to 4.3x10(-11), top SNP rs1900004). The meta-analysis also provided suggestive evidence for association for the cup area at rs690037, P=1.5x10(-7), in the gene RFTN1. Direct sequencing of ATOH7 in 12 patients with optic nerve hypoplasia, one of the leading causes of blindness in children, revealed two novel non-synonymous mutations (Arg65Gly, Ala47Thr) which were not found in 90 unrelated controls (combined Fisher's exact P=0.0136). Furthermore, the Arg65Gly variant was found to have very low frequency (0.00066) in an additional set of 672 controls.

WITHIN the last several years there have been scattered reports of purpura occurring in patients receiving chlorothiazide and hydrochlorothiazide.1 2 3 4 5 6 7 Since the conditions for which these drugs are used occur chiefly in the older age groups, purpura in association with the administration of the drugs mentioned above has not been reported in the pediatric literature.Recently, we observed a group of newborn infants with thrombocytopenia whose mothers had neither a platelet deficiency nor detectable anti-platelet antibody in the serum. However, these mothers had received either chlorothiazide, hydrochlorothiazide or methyclothiazide during pregnancy, and the thrombocytopenia in their infants was possibly due to . . .

Early diagnosis and treatment can alter the morbidity and mortality of patients with cystic fibrosis (CF). This conclusion is based on a study of 130 patients in whom the diagnosis was made under the age of 3 months during the 20year period from 1949 to 1969. These patients were observed for a total of 912 patient-years. The patients were segregated into three groups as follows: Group A (63) were diagnosed prior to the development of symptoms; Group B (13) had mild symptoms; Group C (54) were diagnosed during hospitalization. Immediately following the diagnosis all patients were started on a therapeutic program and followed at regular intervals. There were 29 deaths, 11 in Groups A and B, and 18 in Group C, 8 of which occurred under 1 year of age. The present clinical status of the 101 surviving children is an follows: 14 are in excellent condition, 71 have mild disease or are in good health, and 12 are moderately or severely ill and have a poor prognosis. For all the 130 patients the calculated survival rate at age 20 is 77%.

BACKGROUND: Childhood pneumonia has been reported to be associated with the development of bronchiectasis but there are no case-control studies that have examined this. This study examined the relationship between hospital admission for episode(s) of pneumonia and the risk of radiologically proven bronchiectasis. METHODS: A medical record-based case-control study of bronchiectasis in Indigenous children was conducted in Central Australia. Controls (183), matched to cases (61) by gender, age and year of diagnosis, were Indigenous children hospitalized with other conditions. RESULTS: There was a strong association between a history of hospitalized pneumonia and bronchiectasis [odds ratio (OR), 15.2; 95% confidence interval (95% CI) 4.4-52.7]. This was particularly evident in recurrent hospitalized pneumonia (P for trend < 0.01), severe pneumonia episodes with longer hospital stay (P for trend < 0.01), presence of atelectasis (OR 11.9; 95% CI 3.1-45.9) and requirement for oxygen (P for trend < 0.01). The overall number of pneumonia episodes, rather than its site, was associated with bronchiectasis. Although the total number of pneumonia episodes in the first year of life did not increase the risk of bronchiectasis, more severe episodes early in life did. Malnutrition, premature birth and being small for gestational age were more common findings among cases. Breast-feeding appeared to be a protective factor (OR 0.2; 95% CI 0.1-0.7). CONCLUSIONS: Although we cannot fully answer the question of why bronchiectasis is much more common in Indigenous children, we have provided strong evidence of an association between bronchiectasis and severe and recurrent pneumonia episodes in infancy and childhood.

A review of 156 children with a diagnosis of Wilms' tumor seen and treated at the CHMC—CCRF from January 1, 1960 to December 31, 1970 is presented. No demonstrable effect of age at presentation on subsequent prognosis could be identified. A staging system is presented which is readily used and correlates well with prognosis. Ninety-one of 156 children survive without evidence of Wilms' tumor. Sixty-eight of 93 (73%) children who received all therapy at CHMC—CCRF survive. Large primary size and major extra-renal vascular involvement did not affect the prognosis within a given stage. Tumor spill noted at operation requires subsequent whole abdominal irradiation to adequate doses to prevent local abdominal recurrence. A correlation of vascular involvement with pulmonary metastases is made. The incidence, sites, time, and treatment of relapse is presented. Optimum survival for the child with Wilms' tumor requires a thorough interdisciplinary approach of surgical, medical, and radiation oncologists. Careful follow-up is necessary so that when relapse occurs, especially in the lungs, it can be detected at the earliest possible time, assuring the maximum possible salvage in these patients.

FAMILIAL Addison's disease is an uncommon entity. In 1959 Meakin, Nelson and Thorn1 reviewed the literature and found 5 cases of familial Addison's disease documented by steroid studies or autopsy findings,2 3 4 5 6 and reported another case. Since that time 4 additional cases fulfilling their criteria have been reported.7 8 9 10 The association of superficial moniliasis, idiopathic hypoparathyroidism and Addison's disease is even rarer, only 6 cases being found in the literature.11 12 13 14 15 The purpose of this report is to describe a family in which Addison's disease was present in 3 siblings, 1 of whom also had superficial moniliasis, idiopathic hypoparathyroidism and pernicious anemia. We . . .

Abnormalities in the growth plate may lead to short stature and skeletal deformity including Leri Weil syndrome, which has been shown to result from deletions or mutations in the SHOX gene, a homeobox gene located at the pseudoautosomal region of the X and Y chromosome. We studied the expression of SHOX protein, by immunohistochemistry, in human fetal and childhood growth plates and mRNA by in situ hybridization in childhood normal and Leri Weil growth plate. SHOX protein was found in reserve, proliferative, and hypertrophic zones of fetal growth plate from 12 wk to term and childhood control and Leri Weil growth plates. The pattern of immunostaining in the proliferative zone of childhood growth plate was patchy, with more intense uniform immunostaining in the hypertrophic zone. In situ hybridization studies of childhood growth plate demonstrated SHOX mRNA expression throughout the growth plate. No difference in the pattern of SHOX protein or mRNA expression was seen between the control and Leri Weil growth plate. These findings suggest that SHOX plays a role in chondrocyte function in the growth plate.

OBJECTIVES: Crohn's disease (CD) and ulcerative colitis (UC) are the two most common forms of inflammatory bowel disease (IBD), representing a significant health-care burden. A variant in the autophagy gene ATG16L1 (T300A) has been newly identified as a CD susceptibility locus by genome-wide association. Our aim was to assess the contribution of T300A in determining disease susceptibility and phenotype in two independent Australian IBD cohorts and explore the relationship between T300A and known CD risk factors (NOD2[nucleotide-binding oligomerization domain containing 2] status and smoking). METHODS: In total, 669 CD and 543 UC cases, and 1,244 controls (study 1), 154 CD cases and 420 controls (study 2), and 702 unaffected parents from both groups were genotyped. We conducted case-control and family association analyses, and investigated relationships between T300A and disease subgroups and between NOD2 status and cigarette smoking (CD only). RESULTS: The strong association between CD and T300A was confirmed (P < 0.001), with a two-fold increase in disease risk associated with the GG genotype (odds ratio [OR] 1.96, 95% confidence interval [CI] 1.49-2.58), while ileal CD risk was almost three-fold (OR 2.73, CI 1.87-4.0). ATG16L1 and NOD2 were found to contribute independently to CD risk. A greater than seven-fold increased CD risk was observed for current smokers with a GG genotype (vs nonsmoking AA genotype; P < 0.001, OR 7.65, CI 4.21-13.91). A significant inverse association was found between T300A and UC (P= 0.002). This was strongest for patients with extensive, severe disease. CONCLUSIONS: We confirm the strong association between T300A and CD, specifically ileal subphenotype, and also report the first strong association of this variant with UC.

AIMS: A failure of the arousal mechanism is a key feature in the apnoea theory for sudden infant death syndrome (SIDS). In infants studied at an age when the incidence of SIDS is highest, we evaluated whether in utero smoke exposed infants have altered arousal response to standardised auditory stimuli, and/or sleep pattern, as recorded on overnight complex sleep polysomnography. METHODS: A standardised sequence of audiology stimuli was applied binaurally to 20 in utero smoke and non-smoke exposed infants aged 8-12 weeks during a rapid eye movement (REM) and NREM epoch, in a controlled (temperature, position, pacifier use, noise) sleep environment. Infants were monitored for 10-12 hours using complex sleep polysomnography. RESULTS: Five infants exposed to in utero tobacco smoke did not have behavioural arousal response, whereas all non-smoke exposed infants aroused during NREM (p = 0.016). There was, however, no difference in REM sleep, and the groups did not differ in routine overnight complex sleep polysomnography parameters. CONCLUSION: At the age when the incidence of SIDS is at its peak, infants of smoking mothers are less rousable than those of non-smoking mothers in NREM sleep; this may partly explain why such infants are more at risk of SIDS.

Defects in the nuclear envelope or nuclear 'lamina' networks cause disease and can perturb histone posttranslational (epigenetic) regulation. Barrier-to-Autointegration Factor (BAF) is an essential but enigmatic lamina component that binds lamins, LEM-domain proteins, DNA and histone H3 directly. We report that BAF copurified with nuclease-digested mononucleosomes and associated with modified histones in vivo. BAF overexpression significantly reduced global histone H3 acetylation by 18%. In cells that stably overexpressed BAF 3-fold, silencing mark H3-K27-Me1/3 and active marks H4-K16-Ac and H4-Ac5 decreased significantly. Significant increases were also seen for silencing mark H3-K9-Me3, active marks H3-K4-Me2, H3-K9/K14-Ac and H4-K5-Ac and a mark (H3-K79-Me2) associated with both active and silent chromatin. Other increases (H3-S10-P, H3-S28-P and silencing mark H3-K9-Me2) did not reach statistical significance. BAF overexpression also significantly influenced cell cycle distribution. Moreover, BAF associated in vivo with SET/I2PP2A (protein phosphatase 2A inhibitor; blocks H3 dephosphorylation) and G9a (H3-K9 methyltransferase), but showed no detectable association with HDAC1 or HATs. These findings reveal BAF as a novel epigenetic regulator and are discussed in relation to BAF deficiency phenotypes, which include a hereditary progeria syndrome and loss of pluripotency in embryonic stem cells.

OBJECTIVES: Crohn's disease (CD; MIM 266600) is one of the most common forms of inflammatory bowel disease (IBD), and represents a significant burden to health care in developed countries. Our aim was to determine whether a gene in the IBD linkage region on chromosome 19q13, with a role in Paneth cell secretion and T-cell activation, conferred genetic susceptibility to the development of CD. METHODS: In total, 792 CD cases and 1,244 controls of Australian origin (Caucasian) were genotyped for seven single-nucleotide polymorphisms (SNPs) in the gene encoding the intermediate conductance calcium-activated potassium channel protein (KCNN4) at 19q13.2. CD cases were phenotyped using the Montreal classification. The replication set comprised an additional 326 CD cases and 951 population-based Caucasian controls. Analysis of theKCNN4mRNA transcript was carried out using quantitative reverse transcriptase-PCR. RESULTS: KCNN4SNP rs2306801 was associated with CD (primaryP=0.0008, odds ratio (OR) (95% confidence interval (CI)): 0.76 (0.65–0.89); replicationP=0.01, OR (95% CI): 0.77 (0.61–0.97). Stratification by disease location identified the association between SNP rs2306801 and ileal CD (P=0.01). Non-inflamed ileal mucosa from CD patients carrying any of the common disease-predisposingNOD2variants (R702W, G908R, 1007fs) had significantly reduced levels ofKCNN4mRNA expression (P=0.001). KCNN4 protein expression was detected in Paneth cells, and in T cells in inflamed lamina propria. CONCLUSIONS: Our data implicate the role ofKCNN4in ileal CD. The dual roles ofKCNN4in Paneth cell secretion and T-cell activation and also its nature as a potassium channel make it an important and practical therapeutic target.

OBJECTIVE: The purpose of this chapter is to review critically the existing studies on the epidemiology of pediatric wrestling injuries and to discuss suggestions for injury prevention and further research. DATA SOURCES: Data were obtained from the sports medicine and science literature since 1951. Literature searches were performed using the National Library of Medicine, Pubmed, Medline, Grateful Med, Sports Sciences, SportsDiscus. Keywords used included "Wrestling, Wrestle, Wrestling Injuries, Fractures, and Dermatologic". MAIN RESULTS: Only eight prospective or retrospective studies were found dealing with pediatric wrestling injuries and that provided sufficient information to allow the estimation of injury rates. Exposure-based injury rates were between 6.0 and 7.6 injuries per 1,000 athletic-exposures. Injury rates increased with age, experience, and level of participation. The head/spine/trunk was the body region that incurred the greatest frequency of injuries, followed by the upper and lower extremities. CONCLUSIONS: There are several potential areas for decreasing injury risk in wrestlers, including equipment, coaching, officiating and training. However, informed decisions with regard to preventing injuries are dependent upon the quality of the basic epidemiological data available, and at this time, analyses of risk factors and potential preventive measures are lacking.

Leri-Weill syndrome (LWS) is a dominant (pseudoautosomal) skeletal dysplasia with mesomelic short stature and bilateral Madelung deformity, due to dyschondrosteosis of the distal radius. It results from the loss of one copy of the Short Stature Homeobox Gene (SHOX) from the tip of the short arm of the X or Y chromosome. SHOX molecular testing enabled us to evaluate the histopathology of the radial physis in LWS patients with a documented SHOX abnormality. A widespread disorganisation of physeal anatomy was revealed with disruption of the normal parallel columnar arrangement of chondrocytes. Tandem stacking of maturing chondrocytes within columns was replaced by a side-by-side arrangement. The presence of hypertrophic osteoid with micro-enchondromata in the radial metaphysis suggests abnormal endochondral ossification. The Vickers' ligament was confirmed to blend with the triangular fibrocartilage complex (TFCC). This histopathological study demonstrates that the zone of dyschondrosteosis in LWS is characterised by marked disruption of normal physeal chondrocyte processes and that a generalised physeal abnormality is present.

It is becoming increasingly clear that innate immune mediators play a role in regulating adaptive immune responses in asthma pathogenesis. Cockroach exposure is a major risk factor for the development of asthma. In this study we asked whether German cockroach (GC) feces (frass) could initiate an innate immune response. Naive BALB/c mice were challenged with a single intratracheal inhalation of GC frass. Proinflammatory cytokines were significantly increased in the bronchoalveolar lavage fluid at 3 h and were maintained at higher than baseline levels for at least 24 h. Neutrophil migration into the airways was evident as early as 3 h but was maximal between 6 and 24 h postinhalation. The early increase in cytokine expression was independent of TLR2 or TLR4. Newly infiltrated airway neutrophils were responsible for maintaining high levels of cytokines in the airways. Using neutrophils as an early marker of the innate immune response, we show that show that neutrophils isolated from the airways following GC frass inhalation express TLR2 and release cytokines. GC frass directly affected neutrophil cytokine production via TLR2, but not TLR4, as evidenced by the use of TLR-neutralizing Abs and neutrophils from TLR-deficient mice. Activation of cytokine expression occurred via GC frass-induced NF-kappaB translocation and DNA binding. These data show that GC frass contains a TLR2 agonist and, to our knowledge, this is the first report of an allergen directly activating cells of the innate immune system via TLR2 and suggests an important link between innate and adaptive immunity.

The meconium obtained from siblings of patients with cystic fibrosis was studied for its protein content to determine whether this procedure could be used as a marker of the disease in the newborn. Over a 9-year period 196 specimens were studied. Forty-nine of the 196 infant siblings developed cystic fibrosis and only 4 of this group gave a negative protein reaction. In the remaining group of 147, the protein test was positive in 46, but in a lesser amount. Two methods of testing were employed—a trichloracetic acid ring test and a slide agglutination test using antihuman albumin. Random control samples from 1,600 full-term babies yielded negative tests. This presumptive test is suggested as a possible screening method for the detection of cystic fibrosis with a reliability of approximately 90%. The measurement of sweat electrolytes, although difficult and time consuming in the newborn period, appears to be the most reliable technique of detecting cystic fibrosis.

Stable transgene insertion into a host genome irrevocably and unambiguously marks individual cells and all their descendants, i.e., the respective cell clone. Based thereon, retroviral gene marking has become an important tool for investigating the in vivo fate of different cell types, both in animal models and in clinical gene transfer. Moreover, identification of (vector) insertion sites in malignant clones transformed because of insertional activation of proto-oncogenes after experimental as well as therapeutic retroviral gene transfer has resulted in new insights into oncogenic transformation of hematopoietic stem cells (HSCs). However, because of the high sensitivity of the PCR-based methods for insertion site detection, researchers are often confronted with large numbers of different insertion sites/cell clones whose contribution to the given state is hard to judge. A relatively simple ligation-mediated polymerase chain reaction (LM-PCR) method allows the preferential analysis of insertion sites in those cell clones that significantly contributed to the cell pool analyzed. In murine bone marrow transplantation models, we have shown that this method is very useful to analyze the impact of retroviral insertion sites on both malignant and benign clonal dominance of individual repopulating HSC.

is the most common cause of inherited breast and ovarian cancer. Genetic screens to detect carriers of variants can aid in cancer prevention by identifying individuals with a greater cancer risk and can potentially be used to predict the responsiveness of tumours to therapy. Frequently, classification cannot be performed based on traditional approaches such as segregation analyses, including for many missense variants, which are therefore referred to as variants of uncertain significance (VUS). Functional assays provide an important alternative for classification of BRCA1 and BRCA2 VUS. As reviewed here, both of these tumour suppressors promote the maintenance of genome stability via homologous recombination. Thus, related assays may be particularly relevant to cancer risk. Progress in implementing functional assays to assess missense variants of BRCA1 and BRCA2 is considered here, along with current limitations and the path to more impactful assay systems. While functional assays have been developed to independently evaluate BRCA1 and BRCA2 VUS, high-throughput assays with sufficient sensitivity to characterise the large number of identified variants are lacking. Additionally, because of relatively low conservation of certain domains of BRCA1, and of BRCA2, between humans and rodents, heterologous expression in rodent cells may have limited reliability or capacity to assess variants present throughout either protein. Moving forward, it will be important to perform assays in human cell lines with relevance to particular tumour types, and to strengthen risk predictions based on multifactorial statistical analyses that also include available data on cosegregation and tumour pathology.