Implementation and evaluation of clinical exome sequencing in childhood cancer care: The BASIC3 study

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Background: Advances in sequencing technologies allow for provision of genome-scale data to oncologists and geneticists caring for pediatric cancer patients. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional exome sequencing into the care of children with newly diagnosed solid tumors. Methods: Blood and frozen tumor samples obtained at initial surgery are submitted for clinical exome sequencing (target enrollment 280 patients). Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. Identification of germline cancer susceptibility mutations is compared with standard testing practices. Oncologists are surveyed on prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Patients will be followed for two years to assess the clinical utility of exome data. Preferences for reporting this complex information are obtained by interviews and audiorecording of disclosure visits. Results: Initial results reveal that41 of 49 (84%) ethnically diverse families have consented to enroll on study. Adequate tumor samples were available from 35 of 41 patients (85%), including 11 of 15 (73%) patients with CNS tumors and 24 of 26 (92%) with non-CNS tumors. Pathogenic germline cancer susceptibility mutations (TP53, MSH2) were reported in 2 of the first 11 patients, with a medically-actionable mutation in a gene (SCN5A) unrelated to cancer in 1 patient and 0-4 (median of 2) recessive carrier mutations per patient. Between 9 and 33 protein altering mutations (median of 11) have been identified in tumors, including known cancer genes such as TP53 and others with no known link to pediatric cancer. Conclusions: A robust clinical pipeline for exome sequencing of blood and tumor samples has been successfully developed with significant parental interest. Data assessing the clinical utility of both the tumor and constitutional exomes and the preferences of oncologists and parents for reporting of these results are under study. Supported by NHGRI 1U01HG006485.

Synchrotron phase-contrast X-ray imaging reveals fluid dosing dynamics for gene transfer into mouse airways

Although airway gene transfer research in mouse models relies on bolus fluid dosing into the nose or trachea, the dynamics and immediate fate of delivered gene transfer agents are poorly understood. In particular, this is because there are no in vivo methods able to accurately visualize the movement of fluid in small airways of intact animals. Using synchrotron phase-contrast X-ray imaging, we show that the fate of surrogate fluid doses delivered into live mouse airways can now be accurately and non-invasively monitored with high spatial and temporal resolution. This new imaging approach can help explain the non-homogenous distributions of gene expression observed in nasal airway gene transfer studies, suggests that substantial dose losses may occur at deliver into mouse trachea via immediate retrograde fluid motion and shows the influence of the speed of bolus delivery on the relative targeting of conducting and deeper lung airways. These findings provide insight into some of the factors that can influence gene expression in vivo, and this method provides a new approach to documenting and analyzing dose delivery in small-animal models.

Optimisation of a multipartite human immunodeficiency virus based vector system; control of virus infectivity and large-scale production

BACKGROUND

We have previously described a five-plasmid HIV-1 vector system that utilises a codon-optimised gagpol gene. While this system was shown to be safer than systems using proviral type helpers, the titre of virus produced was relatively low. Therefore, a process of optimising all aspects of virus production was initiated.

METHODS

A systematic approach was taken to the optimisation of virus production by transient expression using a five-plasmid packaging system. Codon-manipulation was used to reduce homology between helper and vector constructs. Ultrafiltration and ultracentrifugation were used for large-scale virus production.

RESULTS

We describe codon-optimised reading frames for Tat and Rev and the optimisation of virus production. The optimisation process resulted in an increase in virus titre of 7- to 8-fold. Several other approaches to increasing viral titre described by others proved ineffective in our system after it had been optimised. In addition, we show that by varying the ratio of the GagPol helper construct to vector, the infectivity of the virus could be controlled. The use of a novel codon-optimised HIV-1 GagPol expression construct with reduced homology to vector sequences significantly reduced transfer of gagpol sequences to transduced cells. Virus could be collected in serum-free medium without a significant loss of titre, which facilitated subsequent processing. Processing using a combination of ultrafiltration and ultracentrifugation allowed efficient and rapid processing of litre volumes of virus supernatant.

CONCLUSIONS

By taking a systematic approach to optimising all aspects of our five-plasmid lentiviral vector system we improved titre, safety, large-scale production, and demonstrated that infectivity could be specifically controlled.

Reduced neurocognition in children who snore

Obstructive sleep apnea syndrome (OSAS) has been associated with reduced neurocognitive performance in children, but the underlying etiology is unclear. The aim of this study was to evaluate the relationship between hypoxemia, respiratory arousals, and neurocognitive performance in snoring children referred for adenotonsillectomy. Thirteen snoring children who were referred for evaluation regarding the need for adenotonsillectomy to a children's hospital otolaryngology/respiratory department underwent detailed neurocognitive and polysomnographic (PSG) evaluation. PSGs were evaluated for respiratory abnormalities and compared with 13 nonsnoring control children of similar age who were studied in the same manner. The snoring children had an obstructive respiratory disturbance index within normal range (mean obstructive apnea/hypopnea index, 0.6/hr). Despite this, several domains of neurocognitive function were reduced in the snoring group. These included mean verbal IQ scores (snorers 92.6 vs. nonsnorers 110.2, P < 0.001), mean global IQ scores (snorers 96.7 vs. nonsnorers 110.2, P < 0.005), mean selective attention scores (snorers 46.4 vs. nonsnorers 11.8, P < 0.001), mean sustained attention scores (snorers 8.0 vs. nonsnorers 2.2, P = 0.001), and mean memory index (snorers 95.2 vs. nonsnorers 112.1, P = 0.001). There was a direct relationship between number of mild oxygen desaturations of > or = 3%, obstructive hypopneas with > or = 3% oxygen desaturations, and respiratory arousals and severity of neurocognitive deficits, with the greatest effect being on memory scores. The disruption of sleep in snoring children produced by relatively mild changes in oxygen saturation or by increases in respiratory arousals may have a greater effect on neurocognitive function than hitherto appreciated. A possible explanation for these neurocognitive deficits may be the combination of the chronicity of sleep disruption secondary to snoring which is occurring at a time of rapid neurological development in the first decade of life. Future studies need to confirm the reversal of these relatively mild neurocognitive decrements post adenotonsillectomy.

Acute respiratory infection in patients with cystic fibrosis with mild pulmonary impairment: comparison of two physiotherapy regimens

Chest physiotherapy is an essential part of the management of cystic fibrosis, yet comparatively few studies have investigated the commonly used forms of chest physiotherapy during acute respiratory exacerbations. Fifteen subjects with cystic fibrosis and predominantly mild pulmonary impairment completed a randomised cross-over trial with 24 hours between treatments. The active cycle of breathing techniques (ACBT) assisted by a physiotherapist was compared with the ACBT performed independently by the patient. Measurement outcomes included pulmonary function tests, indirect calorimetry and oximetry parameters. Energy expenditure was not significantly different between the two treatment regimens, though significant improvements in pulmonary function were apparent 24 hours following the therapist-assisted ACBT. In this group of subjects, neither form of treatment proved superior in terms of energy consumption, but a reduction in airways obstruction was observed as a carry-over effect following the therapist-assisted ACBT.

Efficacy of once-daily tobramycin monotherapy for acute pulmonary exacerbations of cystic fibrosis: a preliminary study

Our objective was to compare the efficacy, safety, and microbiology of once-daily intravenous (IV) tobramycin with conventional 8-hourly tobramycin/ceftazidime IV therapy for acute Pseudomonas aeruginosa (PA) pulmonary exacerbations in cystic fibrosis (CF). CF patients with PA-induced pulmonary exacerbations were allocated to receive either once-daily tobramycin (Mono) or conventional therapy with tobramycin/ceftazidime given 8-hourly (Conv). The two longitudinal groups received therapy in a double-blind, randomized manner over a period of 2 years. Tobramycin doses were adjusted to achieve a daily area under the time-concentration curve of 100 mg x hr/L in both groups. Results were assessed for both short-term changes (efficacy and safety after 10 days of IV antibiotics during acute exacerbations) and long-term changes (efficacy, safety, and sputum microbiology between study entry and exit). Pulmonary function tests (PFTs) on admission were similar in both groups. After 10 days of IV antibiotics, absolute mean improvements in percent of predicted PFTs were 12.8, 12.1, and 13.7 for forced expiratory volume in 1 sec (FEV(1)), forced vital capacity (FVC), and forced expired flow between 25--75% of FVC (FEF(25--75%)) in the Conv group (n = 51 admissions) compared to 10.6, 9.9, and 10.6 in the Mono group (n = 47)(P<0.05 for all). Sixteen percent in the Conv group and 15% of patients in the Mono group did not respond to therapy by day 10. Long-term PFT patterns were similar for the Conv and Mono groups. The time between admissions did not differ. The Mono group showed a significant increase in tobramycin minimum inhibitory concentrations (MICs) against PA from study entry to study exit (P = 0.02, n = 27 strains); this failed to reach significance in the Conv group (P = 0.08, n = 25). There was no significant increase in the number of isolates, with MIC> or =8 mg/L in both groups. No short- or long-term changes in audiology or serum creatinine were found in either group. After 10 days of IV therapy, the urinary enzyme N-acetyl-beta-d-glucosaminidase/creatinine ratios increased in both groups (P0.05). This increase was greater in the Conv compared to the Mono group (P < 0.05). We conclude that this pilot study indicates once-daily tobramycin therapy to be as effective and safe as conventional 8-hourly tobramycin/ceftazidime therapy. Combination antibacterial therapy appears to offer no clinical advantage over once-daily tobramycin monotherapy. Tobramycin once-daily monotherapy is a potential alternative to conventional IV antibacterial therapy which deserves further investigation, including the impact on susceptibility of PA to tobramycin.

Airway gene transfer in mouse nasal-airways: importance of identification of epithelial type for assessment of gene transfer

Mouse nasal airways are often used for the assessment of both reporter and cystic fibrosis transmembrane conductance regulator (CFTR) gene transfer to respiratory epithelia. However, the mouse nasal cavity is lined by both olfactory (OE) and respiratory epithelium (RE). Previous gene transfer studies have suggested that OE may be more efficiently transduced by adenoviral vectors than RE. However, to provide data pertinent to CFTR gene transfer in humans, measurements of CFTR function in mice by transepithelial potential difference (TPD) should be directed towards respiratory rather than olfactory epithelium. We report a new technique to mark the position of the TPD sensing cannula tip in the mouse nasal cavity that permitted us to correlate TPD measurements with epithelial cell type. Using this technique, we found TPD values did not discriminate between respiratory and olfactory epithelia. We next assessed relationships between anatomic regions accessed by the TPD cannula and epithelial type. The frequently used insertion depth of approximately 5 mm from the nose tip predominantly recorded the TPD from anterior dorsal olfactory epithelium. Measurement of the TPD of respiratory epithelium in our study was maximized by insertion of the TPD cannula probe to 2.5 mm depth. Because TPD measurements are not sensitive to epithelial type, adequate control of position and TPD catheter insertion depth are required to ensure accurate estimation of CFTR gene transfer into the target RE in the mouse nasal cavity.

Effect of immediate versus slow intrauterine reduction of congenital diaphragmatic hernia on lung development in the sheep: a morphometric analysis of term pulmonary structure and maturity

The incidence of congenital diaphragmatic hernia (CDH) is 1:1,200-5, 000, and the condition is associated with high mortality and morbidity attributed principally to associated pulmonary hypoplasia. One treatment approach has been for intrauterine intervention to induce lung growth to a sufficient level to allow survival at birth. Repair of the hernia in utero has been attempted, using a method of immediate reduction and repair of the hernia (patch) compared to a slow reduction method using a silastic "silo" sewn over the diaphragm defect to contain the hernial contents. In animal studies, this second method has been associated with lower fetal morbidity and mortality. This study, utilizing the sheep model of CDH, focuses on analysis of lung structural development and maturation, comparing the efficacy of the immediate vs. slow methods of hernial repair in preventing/reversing pulmonary hypoplasia. We hypothesized that: a) Both the immediate (patch) and slow (silo) methods of hernia repair performed in the lamb model of CDH will stimulate lung growth and structural development and restore lung structure and maturity towards normal levels by term gestation; b) Effects will be detectable by morphometric measurement of the following parameters: lung volume; parenchyma to nonparenchyma tissue ratio; volume density of connective tissue in nonparenchyma; gas exchange tissue to airspace ratio; gas exchange surface area; capillary loading; alveolar/airspace density; and alveolar perimeter; c) Effects will be seen in all lobes of the lung; and d) There will be no significant difference in lung size or structural parameters between the two groups. Forty-four pregnant ewes were allocated randomly to one of four groups. Fetal lambs in three groups (n = 36) underwent CDH creation at days 72-74 of gestation. Of surviving lambs showing an adequate hernia, 9 were not operated on further, 11 underwent "repair" using a silastic chimney around the hernial contents (slow reduction), and 11 underwent "repair" by a silastic patch over the diaphragmatic defect (immediate reduction). The fourth group were normal controls. All surviving lambs (n = 8 in each group) were delivered by Cesarian section at 141-143 days (term = 145-149 days). Lungs were obtained at autopsy, inflation-fixed, divided into lobes, and sampled, and morphometric analysis was performed. Comparisons were made between these groups and with matched normal controls and CDH untreated animals prepared in conjunction and previously reported. The lungs from the CDH animals treated by both methods of fetal hernia repair showed significant lung growth and structural development and maturation, although they remained significantly hypoplastic compared to normal. There were minor differences in the lung parameters between these two groups, with a tendency for the slow method to provide more normal parameter values. An exception was the increase in lung volume that was greater for the immediate (patch) method, particularly in the left lower lobe. In conclusion, intrauterine hernia repair by both methods is capable of partially reversing total lung and lobar structural hypoplasia and immaturity. The slow reduction method, with reduced potential for mortality and morbidity, is at least as good at reversing pulmonary hypoplasia as the immediate method. Alternative intrauterine interventions to prevent or reverse pulmonary hypoplasia are discussed and compared with the hernia repair methods used in this study.

The human centromeric survival motor neuron gene (SMN2) rescues embryonic lethality in Smn(-/-) mice and results in a mouse with spinal muscular atrophy

Proximal spinal muscular atrophy (SMA) is a common motor neuron disease in humans and in its most severe form causes death by the age of 2 years. It is caused by defects in the telomeric survival motor neuron gene ( SMN1 ), but patients retain at least one copy of a highly homologous gene, centromeric SMN ( SMN2 ). Mice possess only one survival motor neuron gene ( Smn ) whose loss is embryonic lethal. Therefore, to obtain a mouse model of SMA we created transgenic mice that express human SMN2 and mated these onto the null Smn (-/-)background. We show that Smn (-/-); SMN2 mice carrying one or two copies of the transgene have normal numbers of motor neurons at birth, but vastly reduced numbers by postnatal day 5, and subsequently die. This closely resembles a severe type I SMA phenotype in humans and is the first report of an animal model of the disease. Eight copies of the transgene rescues this phenotype in the mice indicating that phenotypic severity can be modulated by SMN2 copy number. These results show that SMA is caused by insufficient SMN production by the SMN2 gene and that increased expression of the SMN2 gene may provide a strategy for treating SMA patients.

Morphometric analysis of preterm fetal pulmonary development in the sheep model of congenital diaphragmatic hernia

Congenital diaphragmatic hernia (CDH) in humans carries high mortality/morbidity attributed to associated pulmonary hypoplasia. An understanding of the effects of CDH on fetal lung growth is important for development of successful treatments. This study aimed to quantitate structural differences between normal and CDH-affected preterm lamb lungs. We hypothesized that (a) pulmonary hypoplasia is present in preterm CDH-affected lungs; (b) the relative degree of pulmonary hypoplasia increases with gestation; and (c) the left upper lobe (LUL) is affected most. Fetal lambs were allocated to two groups. One group underwent surgery (72-74 days gestation) inducing CDH. Both groups (n = 7, n = 7) were delivered by cesarean section at 129 days (term: 145-149). Lungs were obtained at autopsy, were inflation-fixed, processed for histology, and morphometry was performed. Preterm lungs of CDH-affected lambs in comparison to those of normal lambs demonstrated a reduction in the following: lung weight (37.7 g vs. 116.3 g); lung weight:body weight (0.012 vs. 0.040); fixed lung volume (33.6 ml vs. 96.9 ml); gas-exchange surface area (4.56 m(2) vs. 13.70 m(2)); parenchyma:nonparenchyma (59:41 vs. 72:28); and parenchymal airspace:tissue (16:84 vs. 35:65). Non-parenchyma connective tissue was increased (58%), airspaces were more numerous (1077/mm(2)) and smaller (perimeter 76.6 microm), gas-exchange surface density (2394 cm(-1)) was greater and capillary loading (0.04 ml/m(2)) was reduced compared to preterm normal lung (49%; 778/mm(2); 108.7 microm; 2003 cm(-1), 0.11 ml/m(2), respectively). The LUL was affected most. These data quantitate pulmonary hypoplasia in preterm CDH-affected lambs. Comparisons with published data indicate increasing relative hypoplasia as gestation proceeds. Fetal interventions will affect lung development, depending on timing, with intervention still likely to be worthwhile during late gestation.

A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2

Spinal muscular atrophy (SMA) is a recessive disorder characterized by loss of motor neurons in the spinal cord. It is caused by mutations in the telomeric survival motor neuron 1 ( SMN1 ) gene. Alterations within an almost identical copy gene, the centromeric survival motor neuron 2 ( SMN2 ) gene produce no known phenotypic effect. The exons of the two genes differ by just two nucleotides, neither of which alters the encoded amino acids. At the genomic level, only five nucleotides that differentiate the two genes from one another have been reported. The entire genomic sequence of the two genes has not been determined. Thus, differences which might explain why SMN1 is the SMA gene are not readily apparent. In this study, we have completely sequenced and compared genomic clones containing the SMN genes. The two genes show striking similarity, with the homology being unprecedented between two different yet functional genes. The only critical difference in an approximately 32 kb region between the two SMN genes is the C->T base change 6 bp inside exon 7. This alteration but not other variations in the SMN genes affects the splicing pattern of the genes. The majority of the transcript from the SMN1 locus is full length, whereas the majority of the transcript produced by the SMN2 locus lacks exon 7. We suggest that the exon 7 nucleotide change affects the activity of an exon splice enhancer. In SMA patients, the loss of SMN1 but the presence of SMN2 results in low levels of full-length SMN transcript and therefore low SMN protein levels which causes SMA.

Repeated dose inhaled budesonide versus placebo in the treatment of croup

OBJECTIVE

To investigate the efficacy and tolerance of 12-hourly dosing with 2 mg 4 mL-1 of inhaled budesonide versus placebo in patients admitted to hospital with moderate/severe croup.

METHOD

Eighty-two children hospitalised with croup received either 2 mg 4 mL-1 of budesonide or placebo 12 hourly (maximum four doses) via Ventstream nebuliser in a randomised, double-blind manner. Croup scores were performed at 0, 2, 6, 12, 24, 36 and 48 h from initial nebulisation whilst the patient remained hospitalised. Follow-up assessments were made 1 and 3 days after discharge.

RESULTS

Improvement was observed in the budesonide group over the 12-h dosing interval when compared to placebo (P = 0.04). Time to attain a significant clinical improvement was superior in the budesonide group (P = 0.01). Three days after discharge seven of 32 placebo-treated patients and one of 34 budesonide-treated patients had sought further medical follow-up (P = 0.02).

CONCLUSION

Twelve-hourly dosing with inhaled budesonide significantly improved symptoms of croup as well as decreased relapse rates when compared with placebo.

Enhanced in vivo airway gene transfer via transient modification of host barrier properties with a surface-active agent

Effective adenoviral gene therapy requires efficient viral vector entry into epithelial cells. Injured airway epithelia display enhanced gene transfer, reflecting in part increased vector access to protected cell populations and/or protected basolateral membranes. We tested whether adenoviral gene transfer is enhanced by modification of the epithelial barrier in mouse nasal airways with a nonionic detergent (polidocanol, PDOC). In C57BL/6 mice, 1.6 x 10(9) PFU of Ad5CMV LacZ (AdLacZ) instilled into the right nostril produced negligible gene transfer to the nasal epithelium 2 days after dosing, but significant, dose-dependent increases in gene transfer were achieved by pretreatment with PDOC. Permeation of the electron-dense tracer lanthanum into the intercellular junctions of PDOC (0.1%)-treated murine nasal epithelium, but not into intercellular junctions of vehicle controls, is consistent with PDOC-mediated increases in tight junctional permeability. In CF(-/-) mice, significant gene expression was not detectable after exposure to Ad5CBCFTR alone (1.4 x 10(9) PFU in 20 microl; AdCFTR), but PDOC pretreatment prior to AdCFTR instillation produced functional expression of CFTR (measured as deltaPD) 5 days after instillation. Because the development and testing of lung gene therapy will principally occur in children and adults with airway disease, AdLacZ gene transfer with and without PDOC pretreatment was examined in infected nasal airways. Gene expression was significantly reduced in infected as compared with uninfected airways. We conclude that the use of adjuvant surface-active and/or membrane-perturbing agents, synthetic or naturally derived, may provide a novel approach to enhancing the efficiency of adenoviral gene transfer.

Intragenic telSMN mutations: frequency, distribution, evidence of a founder effect, and modification of the spinal muscular atrophy phenotype by cenSMN copy number

The autosomal recessive neuromuscular disorder proximal spinal muscular atrophy (SMA) is caused by the loss or mutation of the survival motor neuron (SMN) gene, which exists in two nearly identical copies, telomeric SMN (telSMN) and centromeric SMN (cenSMN). Exon 7 of the telSMN gene is homozygously absent in approximately 95% of SMA patients, whereas loss of cenSMN does not cause SMA. We searched for other telSMN mutations among 23 SMA compound heterozygotes, using heteroduplex analysis. We identified telSMN mutations in 11 of these unrelated SMA-like individuals who carry a single copy of telSMN: these include two frameshift mutations (800ins11 and 542delGT) and three missense mutations (A2G, S262I, and T274I). The telSMN mutations identified to date cluster at the 3' end, in a region containing sites for SMN oligomerization and binding of Sm proteins. Interestingly, the novel A2G missense mutation occurs outside this conserved carboxy-terminal domain, closely upstream of an SIP1 (SMN-interacting protein 1) binding site. In three patients, the A2G mutation was found to be on the same allele as a rare polymorphism in the 5' UTR, providing evidence for a founder chromosome; Ag1-CA marker data also support evidence of an ancestral origin for the 800ins11 and 542delGT mutations. We note that telSMN missense mutations are associated with milder disease in our patients and that the severe type I SMA phenotype caused by frameshift mutations can be ameliorated by an increase in cenSMN gene copy number.

Diagnosis of spinal muscular atrophy in an SMN non-deletion patient using a quantitative PCR screen and mutation analysis

We report a child with clinical findings consistent with Werdnig-Hoffmann disease (spinal muscular atrophy type I) who was found not to have the homozygous absence of the survival motor neurone (SMN(T)) gene observed in approximately 95% of spinal muscular atrophy patients. A quantitative PCR based dosage assay for SMN(T) copy number showed that this patient possessed a single copy of the SMN(T) gene. Heteroduplex and sequence analysis of the remaining copy of SMN(T) showed a 2 base pair deletion within exon 4 which produces a frameshift and premature termination of the deduced SMN(T) protein. This protocol of initial SMN(T) gene dosage analysis followed by mutation detection allows identification of SMA compound heterozygotes (patients lacking one copy of SMN(T) and having another mutation in their other copy), thereby increasing the sensitivity of SMA molecular diagnosis.