Factors influencing treatment response of pulmonary exacerbation in children with cystic fibrosis

BACKGROUND

Pulmonary exacerbations in cystic fibrosis (CF) significantly impact morbidity and mortality. This study aimed to assess treatment response rates and identify contributing factors towards treatment response.

METHODS

In this single-center, retrospective, longitudinal study spanning four years, we analyzed all pulmonary exacerbation admissions. We compared lung function at baseline, admission, end of treatment, and 6-week follow-up. Treatment response was defined as ≥95% recovery of baseline FEV1%.

RESULTS

There were 78 children who required a total of 184 admissions. The mean duration of treatment was 14.9±2.9 days. FEV1% returned to 95% of baseline in 59% following treatment. The magnitude of the decline in lung function on admission in children who did not respond to treatment was 21.7±15.2% while the decline in children who responded to treatment was 8.3±9.4%, P<0.001. Children who experienced a decline in FEV1% greater than 40% exhibited an 80% reduced likelihood of returning to their baseline values (OR -0.8, 95% CI -0.988; -0.612). Similarly, those with FEV1% reductions in the ranges of 30-39% (OR -0.63, 95% CI -0.821; -0.439), 20-29% (OR -0.52, 95% CI -0.657; -0.383), and 10-19% (OR -0.239, 95% CI -0.33; -0.148) showed progressively lower odds of returning to baseline. Fourty-eight children required readmission within 7.7±5.4 months, children who responded to treatment had a longer time taken to readmission (8.9±6.4 months) versus children who did not respond to treatment (6.4±3.5 months), (OR: -0.20, 95% CI -0.355; -0.048).

CONCLUSIONS

A greater decline in lung function on admission and readmission within 6 months of the initial admission predicts non-response to treatment. This highlights the importance of re-evaluating follow-up strategies following discharge.

Improved survival at the cost of more chronic lung disease? Current management and outcomes in extremely preterm infants born in New South Wales and the Australian Capital Territory: 2010-2020

BACKGROUND

Since 2010, most tertiary care hospitals in Australia have changed how they care for extremely premature infants. However, in-hospital and longer-term outcome data have suggested unchanged or even worse health outcomes in later epochs, especially respiratory outcomes. This study examined the trend in outcomes since these changes were introduced, particularly the prevalence of chronic neonatal lung disease (CLD).

METHODS

This is a retrospective cross-sectional analysis of data from the Neonatal Intensive Care Units' (NICUS) database of all perinatal intensive care units in New South Wales and the Australian Capital Territory, including infants born at ≥ 24 and ≤ 28 weeks of gestational age in tertiary perinatal units between January 1, 2010, and December 31, 2020. Temporal trends and changes in primary outcome were examined by linear and adjusted multivariable logistic regression models.

RESULTS

This study included 3258 infants. We saw significant changes in antenatal magnesium sulfate (75% increase), delayed cord clamping (66% increase), delivery room intubations (30% decrease), any time (20% decrease), duration on mechanical ventilation (100-hour decrease), and hours on noninvasive ventilation (200-hour increase). Mortality decreased from 17% to 6%. The incidence of CLD increased significantly even when adjusted for confounders (15% increase). Any time and mean hours spent on mechanical ventilation significantly increased the odds of CLD. This study could not find a significant association of any of the protective antenatal treatments on CLD.

CONCLUSIONS

The last decade saw a significant improvement in survival and survival to discharge without major morbidity. There was increased use of magnesium sulfate, delayed cord clamping, and less invasive respiratory management of extremely preterm infants. The avoidance of mechanical ventilation may impact the incidence of CLD.

Is perinatal substance abuse falling through the cracks?

OBJECTIVES

Perinatal substance abuse (PSA) is associated with increased risk of prematurity, low birth weight, neonatal abstinence syndrome, behavioral issues and learning difficulties. It is imperative that robust care pathways are in place for these high-risk pregnancies and that staff and patient education are optimized. The present study explores the knowledge and attitudes of healthcare professionals toward PSA to identify knowledge gaps to enhance care and reduce stigma.

METHODS

This is a cross-sectional study using questionnaires to survey healthcare professionals (HCPs) working in a tertiary maternity unit (n = 172).

RESULTS

The majority of HCPs were not confident in the antenatal management (75.6%, n = 130) or postnatal management (67.5%, n = 116) of PSA. More than half of HCPs surveyed (53.5%, n = 92) did not know the referral pathway and 32% (n = 55) did not know when to make a TUSLA referral. The vast majority (96.5%, n = 166) felt that they would benefit from further training, and 94.8% (n = 163) agreed or strongly agreed that the unit would benefit from a drug liaison midwife. Among study participants, 54.1% (n = 93) agreed or strongly agreed that PSA should be considered a form of child abuse and 58.7% (n = 101) believe that the mother is responsible for damage done to her child.

CONCLUSIONS

Our study highlights the urgent need for increased training on PSA to enhance care and reduce stigma. It is imperative that staff training, drug liaison midwives and dedicated clinics are introduced to hospitals as a matter of high priority.

Measurement of Direct-Photon Cross Section and Double-Helicity Asymmetry at sqrt[s]=510 GeV in p[over →]+p[over →] Collisions

We present measurements of the cross section and double-helicity asymmetry A_{LL} of direct-photon production in p[over →]+p[over →] collisions at sqrt[s]=510  GeV. The measurements have been performed at midrapidity (|η|<0.25) with the PHENIX detector at the Relativistic Heavy Ion Collider. At relativistic energies, direct photons are dominantly produced from the initial quark-gluon hard scattering and do not interact via the strong force at leading order. Therefore, at sqrt[s]=510  GeV, where leading-order-effects dominate, these measurements provide clean and direct access to the gluon helicity in the polarized proton in the gluon-momentum-fraction range 0.02<x<0.08, with direct sensitivity to the sign of the gluon contribution.

Examining the impact of premature birth on parental mental health and family functioning in the years following hospital discharge: A review

BACKGROUND

This review provides an update of the current research related to the impact of extreme and very premature birth on parental mental health and family functioning following discharge from hospital.

METHODS

Full-text peer reviewed articles in English, describing parents' and families' health and wellbeing after the discharge from hospital of their baby using validated questionnaires, were evaluated. Results of included studies are presented in a summarized format. Embase, Medline and PsycINFO databases were accessed in January 2021.

RESULTS

38 studies were included. Nine manuscripts reported on parental mental health and 13 on stress, which are a concern after the birth of a premature infant, especially in the first year. Depression, anxiety, and stress are known to measure higher compared to parents of infants born at term. Over several years, these measures of mental health decrease significantly. Four reported on quality of life for parents of premature infants, which is reduced immediately after discharge, but then improves over time. The impact of premature birth on the family functioning was described in ten included studies and was described to have positive and negative consequences.

CONCLUSION

The negative impact of the premature birth and hospital journey on parental mental health lessens significantly with time.

Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes

Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers (ZNF217 and SYPL1) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies.

Breast cancer heterogeneity and tumour evolutionary trajectories remain largely unknown among women of African ancestry. Here, the authors perform whole genome and transcriptome sequencing of Nigerian breast cancer patients and identify unique evolutionary phenomena.

Probing Gluon Spin-Momentum Correlations in Transversely Polarized Protons through Midrapidity Isolated Direct Photons in p^{↑}+p Collisions at sqrt[s]=200 GeV

Studying spin-momentum correlations in hadronic collisions offers a glimpse into a three-dimensional picture of proton structure. The transverse single-spin asymmetry for midrapidity isolated direct photons in p^{↑}+p collisions at sqrt[s]=200  GeV is measured with the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). Because direct photons in particular are produced from the hard scattering and do not interact via the strong force, this measurement is a clean probe of initial-state spin-momentum correlations inside the proton and is in particular sensitive to gluon interference effects within the proton. This is the first time direct photons have been used as a probe of spin-momentum correlations at RHIC. The uncertainties on the results are a 50-fold improvement with respect to those of the one prior measurement for the same observable, from the Fermilab E704 experiment. These results constrain gluon spin-momentum correlations in transversely polarized protons.

Survey of the practices of neonatologists in managing neonates believed to be at high risk of sleep disordered breathing

OBJECTIVE

To determine the practices of neonatologists in managing high-risk neonates believed to be at risk of sleep disordered breathing (SDB).

DESIGN

An electronic web-based questionnaire assessing awareness of and current practices for managing neonates predisposed to SDB with conditions like craniofacial anomalies, neuromuscular disorders or airway problems was emailed to 232 neonatologists and neonatal fellows working in Australia and New Zealand (NZ). Additionally, neonatologists were approached directly during the annual Australia and NZ perinatal conference in 2019.

RESULTS

93 neonatologists (40%) responded to the survey. The majority (85%) of the respondents stated that there were no written protocols/criteria for sleep consultation in their unit. We found considerable variations in the threshold for performing tests including oximetry or referring for polysomnography. Most respondents would perform oximetry before referring for a sleep consultation. However, the duration of oximetry varied from 6 to 24 hours and there was no consensus about what is considered abnormal on an oximetry study.

CONCLUSION

Management of SDB is gaining importance in neonatal care because of prolonged length of hospital stay and possible long-term effects of SDB. Responses received suggest a lack of clarity regarding thresholds for referral for treatment of SDB. Likely contributory factors are concerns regarding a lack of long-term outcome data from treatment perceived to be onerous for the family, unsettling to some infants and delaying hospital discharge. To overcome inconsistencies in practice, standardised guidelines for assessing and managing SDB in neonates are needed.

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content. Furthermore, STARR-seq readout is confounded by RNA secondary structure and thermodynamic stability. To address these potential confounders, we developed a negative binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. Moreover, to aid our effort, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to comprehensively and unbiasedly call enhancers in them.

Response of Very Premature Infants with Bronchopulmonary Dysplasia to Inhaled Salbutamol

Bronchopulmonary Dysplasia (BPD) is the most common chronic respiratory disease found in premature infants following prolonged supplemental oxygen and mechanical ventilation. Although salbutamol, a selective ß2 agonist, is known to relax the hypertrophied smooth muscles around the small airways in adults, earlier literature has suggested that neonates did not have enough peribronchial smooth muscle for constriction and thus lacked a bronchodilatory response to ß2 agonists. The present study was designed to determine whether infants of less than 32 weeks gestational age with elevated lung resistance were responsive to salbutamol. Nineteen premature infants (mean gestational age 26.0 +/- 2.1 weeks and mean birth weight 851.3 +/- 244.4 g) were recruited for the study. Immediately before and 30 minutes after the commencement of nebulized salbutamol administration, a minimum of 15 breaths were measured and analyzed for each patient. From this breath-by-breath analysis, the lung mechanics and Work of Breathing (WOB) were calculated. Results were then compared by paired t-tests. The use of salbutamol resulted in a significant improvement in airway resistance (p = 0.008) and tendency for impedance reduction. These results indicate that very premature infants (< 32 weeks) with BPD respond favorably to bronchodilators. Although the mechanism of action remains to be elucidated, salbutamol most probably achieves its effects through the relaxation of the hypertrophied peribronchial smooth muscle. Early intervention to relieve airway obstruction may promote early weaning from mechanical ventilation and diminish both duration and severity of BPD.

An integrative ENCODE resource for cancer genomics

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.

Sleep disordered breathing (SDB) in neonates and implications for its long-term impact

Sleep-disordered breathing (SDB) is a significant cause of morbidity in neonates and young infants. SDB occurs more commonly in preterm infants and in neonates with underlying syndromes. Recent evidence shows that infants with obstructive sleep apnoea (OSA) or SDB have greater health care resource utilization, including longer hospital stay. Management of SDB includes non-invasive ventilation or surgical interventions tailored to the patient. Screening high risk newborns should allow for early diagnosis and timely therapeutic intervention for this population. However, the thresholds for diagnosing SDB and for guiding and implementing treatment in neonates remain unclear. A collective effort is required to standardize the practice worldwide. This article will discuss neonatal sleep physiology and characteristics of neonatal sleep, with an emphasis on the epidemiology and diagnosis of SDB in neonates and its implications for long term outcomes.

Abstract LB-300: The life history of breast cancer in Nigerian women: Evidence for ethnic differences in tumor evolution based on whole-genome sequencing

Breast cancer is a heterogeneous disease and the incidence to mortality ratio is highest for women of African ancestry. Paucity of data from non-European ancestry groups limits our understanding of the underlying etiological differences or alternative routes to progression that may explain differential outcomes. To examine the contribution of genomic differences, we performed high-depth whole-genome sequencing on 100 breast tumors (90X) and their paired normal samples (30X) from indigenous African women with breast cancer in Southwest Nigeria and performed comparative analysis with 84 TCGA whole genome sequences of breast tumor/normal pairs (46 White, 30 African American and 8 samples representing other ethnicities). High confidence somatic single nucleotide variants (SNVs) were obtained by using MuTect and Strelka. To analyse intra-tumoral heterogeneity (ITH), Battenberg and DPClust were used to call copy number aberrations (CNA) and cluster somatic SNVs based on cancer cell fraction (CCF) respectively. We find that in the HR-/HER2+ subtype, clonal losses of chromosome 14q are highly enriched in Nigerians (41%) but absent in the Whites even though the proportion of this subtype was comparable between the two groups (42% and 33% respectively). This is an interesting observation since not only 14q loss is known to be an event associated with breast cancer aggressiveness, but HR-/HER2+ has also been reported to be enriched within the relatively younger Nigerian patients with breast cancer. This may in part explain inter-ethnic disparity in survival. Also, somatic SNV clustering analysis showed that Nigerian cancers have a higher level of ITH than Whites, which may explain the pronounced aggressiveness of breast cancer in women of African ancestry. In contrast, early drivers (e.g. TP53 and PIK3CA) and whole genome duplication rates were mostly similar between the groups. Our observations suggest differences in the underlying evolutionary trajectories of breast cancer across ethnic backgrounds. These data underscore the need for larger and more in-depth studies of diverse cancer genomes and, if validated, may translate into clinical intervention opportunities tailored to women of African ancestry and accelerate progress in precision cancer care.

Note: This abstract was not presented at the meeting.

Citation Format: Naser Ansari-Pour, Jason J. Pitt, Stefan Dentro, Dominic Fitzgerald, Yonglan Zheng, Toshio F. Yoshimatsu, Padma Rajagopal, Andreas Gruber, Ayodele Sanni, Olayiwola Oluwasola, Mustapha Ajani, Abayomi Odetunde, Abiodun Popoola, Adeyinka Falusi, Temidayo Ogundiran, John Obafunwa, Oladosu Ojengbede, Nasiru Ibrahim, Kevin P. White, Dezheng Huo, Peter Van Loo, David C. Wedge, Olufunmilayo Olopade. The life history of breast cancer in Nigerian women: Evidence for ethnic differences in tumor evolution based on whole-genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-300.

Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria

Somatic mutation signatures may represent footprints of genetic and environmental exposures that cause different cancer. Few studies have comprehensively examined their association with germline variants, and none in an indigenous African population. SomaticSignatures was employed to extract mutation signatures based on whole-genome or whole-exome sequencing data from female patients with breast cancer (TCGA, training set, n = 1,011; Nigerian samples, validation set, n = 170), and to estimate contributions of signatures in each sample. Association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants were examined using linear regression. Nine stable signatures were inferred, and four signatures (APOBEC C>T, APOBEC C>G, aging and homologous recombination deficiency) were highly similar to known COSMIC signatures and explained the majority (60-85%) of signature contributions. There were significant heritable components associated with APOBEC C>T signature (h² = 0.575, p = 0.010) and the combined APOBEC signatures (h² = 0.432, p = 0.042). In TCGA dataset, seven common SNPs within or near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21-0.45) of APOBEC signature contribution at genome-wide significance, while rare germline mutations in MTCL1 was also significantly associated with a higher contribution of this signature (p = 6.1 × 10^-6 ). This is the first study to identify associations between germline variants and mutational patterns in breast cancer across diverse populations and geography. The findings provide evidence to substantiate causal links between germline genetic risk variants and carcinogenesis.

The efficacy and safety of velagliflozin over 16 weeks as a treatment for insulin dysregulation in ponies

BACKGROUND

A previous six-week (wk) study demonstrated the potential of the sodium-glucose linked transport inhibitor velagliflozin as a novel treatment for equine insulin dysregulation. The present study examined the safety and efficacy of velagliflozin over 16 wk. of treatment, and over 4 wk. of withdrawal. Twenty-four insulin dysregulated ponies were selected, based on their hyper-responsiveness to a diet challenge meal containing 3.8 g non-structural carbohydrates (NSC)/kg bodyweight (BW). Ponies with serum insulin > 90 μIU/mL either 2 or 4 h after feeding were enrolled, and randomly allocated to receive either velagliflozin (0.3 mg/kg BW orally once daily, n = 12), or a placebo (n = 10-12) for 16 wk. The subjects were fed 7.5 g NSC/kg BW/day to maintain a fat body condition. Safety was assessed through daily monitoring, veterinary examination, and the measurement of fasting blood glucose, biochemistry and haematology. Efficacy at reducing post-prandial hyperinsulinemia was assessed using a diet challenge every 8 wk. during treatment and 4 wk. after withdrawal.

RESULTS

Velagliflozin was well accepted by all subjects and caused no adverse effects or hypoglycaemia. Post-prandial serum insulin (insulin Cmax) did not change significantly in the control animals over the entire study period (P = 0.101). In contrast, insulin Cmax (mean ± SE) concentrations fell over time in the velagliflozin-treated group from 205 ± 25 μIU/mL in wk. 0, to 119 ± 19 μIU/mL (P = 0.015) and 117 ± 15 μIU/ml (P = 0.029) after 8 and 16 wk. of treatment, respectively. Although the insulin Cmax in this group was not significantly lower than in controls at wk-8 (P = 0.061), it was lower at wk-16 (P = 0.003), and all 12 treated ponies were below the previously-determined risk threshold for laminitis at this time. After 4 wk. withdrawal, the insulin Cmax returned to 199 ± 36 μIU/mL in the treated group, with no rebound effect.

CONCLUSIONS

Velagliflozin appears to be a promising and safe treatment for equine insulin dysregulation, bringing post-prandial insulin concentrations below the laminitis risk threshold, albeit without normalising them.

Comprehensive functional genomic resource and integrative model for the human brain

Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions. Integration shows that varying cell-type proportions largely account for the cross-population variation in expression (with >88% reconstruction accuracy). It also allows building of a gene regulatory network, linking genome-wide association study variants to genes (e.g., 321 for schizophrenia). We embed this network into an interpretable deep-learning model, which improves disease prediction by ~6-fold versus polygenic risk scores and identifies key genes and pathways in psychiatric disorders.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.

Author Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc. Chicago, IL, USA was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.

The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes

A number of studies indicate that rare copy number variations (CNVs) contribute to the risk of schizophrenia (SCZ). Most of these studies have focused on protein-coding genes residing in the CNVs. Here, we investigated long noncoding RNAs (lncRNAs) within 10 SCZ risk-associated CNV deletion regions (CNV-lncRNAs) and examined their potential contribution to SCZ risk. We used RNA sequencing transcriptome data derived from postmortem brain tissue from control individuals without psychiatric disease as part of the PsychENCODE BrainGVEX and Developmental Capstone projects. We carried out weighted gene coexpression network analysis to identify protein-coding genes coexpressed with CNV-lncRNAs in the human brain. We identified one neuronal function-related coexpression module shared by both datasets. This module contained a lncRNA called DGCR5 within the 22q11.2 CNV region, which was identified as a hub gene. Protein-coding genes associated with SCZ genome-wide association study signals, de novo mutations, or differential expression were also contained in this neuronal module. Using DGCR5 knockdown and overexpression experiments in human neural progenitor cells derived from human induced pluripotent stem cells, we identified a potential role for DGCR5 in regulating certain SCZ-related genes.

The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders

Schizophrenia and bipolar disorder are complex psychiatric diseases with risks contributed by multiple genes. Dysregulation of gene expression has been implicated in these disorders, but little is known about such dysregulation in the human brain. We analyzed three transcriptome datasets from 394 postmortem brain tissue samples from patients with schizophrenia or bipolar disorder or from healthy control individuals without a known history of psychiatric disease. We built genome-wide coexpression networks that included microRNAs (miRNAs). We identified a coexpression network module that was differentially expressed in the brain tissue from patients compared to healthy control individuals. This module contained genes that were principally involved in glial and neural cell genesis and glial cell differentiation, and included schizophrenia risk genes carrying rare variants. This module included five miRNAs and 545 mRNAs, with six transcription factors serving as hub genes in this module. We found that the most connected transcription factor gene POU3F2, also identified on a genome-wide association study for bipolar disorder, could regulate the miRNA hsa-miR-320e and other putative target mRNAs. These regulatory relationships were replicated using PsychENCODE/BrainGVEX datasets and validated by knockdown and overexpression experiments in SH-SY5Y cells and human neural progenitor cells in vitro. Thus, we identified a brain gene expression module that was enriched for rare coding variants in genes associated with schizophrenia and that contained the putative bipolar disorder risk gene POU3F2 The transcription factor POU3F2 may be a key regulator of gene expression in this disease-associated gene coexpression module.

Surgery in nontuberculous mycobacteria pulmonary disease

Medical treatment of pulmonary nontuberculous mycobacteria (NTM) disease has highly variable outcomes. Despite the use of multiple antibiotics, sputum clearance is often difficult to achieve, especially in cases with macrolide resistant NTM infection. Immunocompromised patients and those with structural lung disease are at increased risk, although occurrence in immunocompetent patients without structural lung disease is well recognised. Most pulmonary NTM disease involves Mycobacterium avium complex (MAC), but with enhanced identification multiple species have now been recognised as opportunistic pathogens. The observed increase in NTM disease, especially infection with multidrug-resistant Mycobacterium abscessus complex, is probably multifactorial. Surgery has been used as adjuvant treatment in patients with 1) focal disease that can be removed or 2) bothersome symptoms despite medical treatment that can be ameliorated. Early post-surgical mortality is low, but long-term morbidity and mortality are highly dependent on the degree of lung involvement and the residual lung function, the potency of medical treatment and the type of surgical intervention. In conjunction with antibiotic therapy, reported post-surgical sputum clearance was excellent, although publication bias should be considered. Bronchopleural fistulae were problematic, especially in pneumonectomy cases. Study results support the use of minimal resection surgery, in a carefully selected subgroup of patients with focal disease or persistent symptoms.

Educational aims

To critically review the literature describing the use of surgery in the treatment of pulmonary disease caused by nontuberculous mycobacteria (NTM).To assess the outcomes and complications observed with different surgical approaches used in the treatment of pulmonary NTM disease.

Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology. GATA3 mutations are also more frequent in Nigerians regardless of subtype. Higher proportions of APOBEC-mediated substitutions strongly associate with PIK3CA and CDH1 mutations, which are underrepresented in Nigerians and Blacks. PLK2, KDM6A, and B2M are also identified as previously unreported significantly mutated genes in breast cancer. This dataset provides novel insights into potential molecular mechanisms underlying outcome disparities and lay a foundation for deployment of precision therapeutics in underserved populations.

Abstract 287: Germline variants and somatic mutation signatures in breast cancer across populations of African and European ancestry

Background: Somatic mutation signatures may represent the footprints of genetic and environmental exposures that cause different types of cancer. However, few studies have comprehensively examined the association between germline variants and somatic mutation signatures, and none in African ancestry populations. Methods: Study samples consist of 1,011 breast cancer patients from The Cancer Genome Atlas (TCGA; 168 Black, 737 White, and 106 other ancestries, discovery set) and 170 Nigerian women with breast cancer (validation set). SomaticSignatures was employed to extract mutation signatures from whole-genome or whole-exome sequenicng data, and to estimate contributions of signatures on each sample. SNPtest and SKAT-O were used to conduct association tests for the association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants. SNP array-based heritability was calculated by GCTA. Results: Nine stable signatures were inferred in total. Four of them – APOBEC C&gt;T, APOBEC C&gt;G, aging, and homologous recombination deficiency (HRD) – were highly similar to known COSMIC signatures. These together explained the vast majority (60%~85%) of mutation signature contributions regardless of race/ethnicity or tumor subtype. The heritability estimates displayed significantly heritable components for APOBEC C&gt;T signature (h2 = 0.575, P = 0.010) and combined APOBEC signature (h2 = 0.432, P = 0.042). In TCGA dataset, seven common SNPs on/near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21~0.45) of APOBEC signature contribution at genome-wide significance, while rare deleterious variants in MTCL1 and HIV-EP1 were also significantly associated with this signature contribution (P =1.9×10-6, 2.2×10-5, respectively). The combined rare deleterious variants in BRCA1 and BRCA2 were significantly correlated with the contribution of HRD signature (P =1.0×10-8, 1.1×10-5, respectively). In the Nigerian cohort, only the associations in HIV-EP1 and BRCA2 were replicated with relatively higher mutation frequencies (N = 9, 8; P = 0.05, 0.01, respectively). In addition, the combined rare deleterious variants in HRD pathway genes was significantly associated with the contribution of HRD signature in both TCGA (P = 2.8×10-5) and Nigerian samples (P = 0.01). After excluding BRCA1/2, this association turned to be nonsignificant. Conclusion: Our study identified associations between germline variants and mutational patterns in breast cancer across different ethnicities, especially in African women for the first time. This finding has important public health implications as it provides evidence to substantiate causal links between germline genetic variants and carcinogenesis process. Further replications in larger and diverse populations are needed.

Citation Format: Shengfeng Wang, Jason J. Pitt, Yonglan Zheng, Toshio F. Yoshimatsu, Guimin Gao, Markus Riester, Ayodele Sanni, Olayiwola Oluwasola, Dominic Fitzgerald, Temidayo Ogundiran, Chinedum Babalola, Abiodun Popoola, Adeyinka Falusi, Wendy Winckler, John Obafunwa, Oladosu Ojengbede, Nasiru Ibrahim, WABCS Working Group, Jordi Barretina, Kevin P. White, Dezheng Huo, Olufunmilayo I. Olopade. Germline variants and somatic mutation signatures in breast cancer across populations of African and European ancestry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 287.

The influence of sleep and training load on illness in nationally competitive male Australian Football athletes: A cohort study over one season

OBJECTIVES

To determine the incidence of illness, and identify the relationship between sleep, training load and illness in nationally competitive Australian football athletes. Second, to assess multivariate effect between training load and/or sleep variables.

DESIGN

Cohort study.

METHODS

Retrospective analyses of prospectively collected cohort data were conducted on forty-four male athletes over a 46-week season. The primary outcome was illness incidence, recorded daily by medical doctors. Independent variables were acute, chronic and acute:chronic ratios of: sleep quality, sleep quantity, internal training load and external training load defined as: total running distance, high speed running distance and sprint distance. Generalised estimating equations using Poisson (count) models were fit to examine both univariate and multivariate associations between independent variables and illness incidence.

RESULTS

67 incidences of illness were recorded, with an incidence rate of 11 illnesses per 1000 running hours. Univariate analysis showed acute and chronic sleep hours and quality, as well as acute sprint and total running distance to be significantly associated with illness. Multivariate analysis identified that only acute sleep quantity was significantly, negatively associated with illness incidence (OR 0.49, CI 0.25-0.94) once all univariate significant variables were controlled for. There was no relationship between external training load and illness when sleep metrics were controlled for.

CONCLUSIONS

In a cohort of Australian football athletes, whose load was well monitored, reduced sleep quantity was associated with increased incidence of illness within the next 7 days. Monitoring sleep parameters may assist in identifying individuals at risk of illness.

Comparison of facemask and mouthpiece interfaces for multiple breath washout measurements

BACKGROUND

Different interfaces (mouthpiece/nose clip vs. facemask) are used during multiple breath washout (MBW) tests in young children.

METHODS

We investigated the effect of interface choice and breathing modalities on MBW outcomes in healthy adults and preschool children.

RESULTS

In adults (n = 26) facemask breathing significantly increased LCI, compared to mouthpiece use (mean difference (95% CI) 0.4 (0.2; 0.6)), with results generalizable across sites and different equipment. Exclusively nasal breathing within the facemask increased LCI, as compared to oral breathing. In preschoolers (2-6 years, n = 46), no significant inter-test difference was observed across interfaces for LCI or FRC. Feasibility and breathing stability were significantly greater with facemask (incorporating dead space volume minimization), vs. mouthpiece. This was more pronounced in subjects <4 years of age.

CONCLUSION

Both nasal vs. oral breathing and mouthpiece vs. facemask affect LCI measurements in adults. This effect was minimal in preschool children, where switching between interfaces is most likely to occur.

Acroangiodermatitis mimicking Kaposi's sarcoma in an HIV-positive man

Kaposi's sarcoma (KS) is the commonest human immunodeficiency virus (HIV)-related malignancy with its characteristic cutaneous morphological appearance and histopathological features. However, it can be simulated by other co-morbid opportunistic infections and unrelated dermatological conditions. We describe such a case of acroangiodermatitis in an HIV co-infected man, based on exclusion of KS histologically and the absence of human herpesvirus 8, the causative agent of KS.

Abstract P1-06-03: Serial evolution of hormone receptor status and mutational profile among patients with metastatic breast cancer

Introduction: Tumor heterogeneity presents a significant impediment to identifying appropriate treatments for patients. Genetic mutations and hormone receptors are frequently used as a guide for selecting appropriate targeted or hormonal therapies, however it is possible that these markers may change over time, leading to reduced effectiveness of these treatments. In this study, we review the results of serial and paired biopsies to identify receptor switch in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status as well as to identify changes in clinically relevant mutations, including spatial and temporal heterogeneity.

Methods: We identified a total of 237 patients initially presenting with ER+/HER2 negative breast cancer and who had multiple biopsies during the course of their treatment, including at least one in the metastatic setting. ER, PR, and HER2 status for each of these serial biopsies was gathered from chart reviews. HER2 results by both IHC and FISH were collected. PIK3CA mutations were also assessed by Snapshot utilizing multiplexed PCR of common hotspot mutations using DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue.

Results: From a total of 213 patients with known ER status for multiple serial biopsies, we identified 9.4% (N=20) who had at least one change in ER status over time. From a total of 198 patients who had documented PR status for multiple biopsies, 40.4% (N=80) had at least one change in PR status. Changes in HER2 status were similarly assessed, with 6.7% of patients having at least one change by IHC and 4.4% of patients having at least one change by FISH. Of those patients exhibiting changes in ER status, 6 were noted to have multiple changes over time. Of those with changes in PR status, 18 had multiple changes over time. Changes in hormone receptor status were also noted to occur between serial biopsies in the metastatic setting. A total of 128 patients had ER results available for multiple metastatic specimens, of which 8.6% (N=11) had at least one change in ER status. A total of 116 patients had PR results available for multiple metastatic biopsies, of which 38.8% (N=45) had at least one change in PR status. Changes were also noted in the metastatic setting in HER2 (IHC) with a frequency of 8.7% and in HER2 (FISH) with a frequency of 4.7%. A subset of 108 patients were identified as harboring a mutation in PIK3CA. Within this population, 9.6% of patients had at least one change in ER status over time and 34.1% had at least one change in PR status. 9.0% exhibited at least one change in HER2 (IHC) and 6.5% in HER2 (FISH). Serial changes in genotype, from pre- and post-treatment biopsies, were also detected using NGS based Foundation Medicine platform, including acquired alterations in the ESR1 and PI3K pathway.

Conclusion: Serial changes in hormone receptor status and mutation profile are not uncommon among patients initially diagnosed with ER+/HER2 negative breast cancer, and some patients have been noted to have multiple changes over time. Further studies are needed to understand the mechanistic underpinnings governing the emergence of these alterations and their relationship to therapeutic resistance in breast cancer.

Citation Format: Henderson L, Brachtel E, Fitzgerald D, Gadd M, Specht M, Thabet A, Gurski J, Sgroi D, Moy B, Isakoff S, Bardia A, Juric D. Serial evolution of hormone receptor status and mutational profile among patients with metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-03.

Group Embedded Figures Test: Normative Data for Male Automotive Mechanical Apprentice Tradesmen

The Group Embedded Figures Test was administered to 274 male students enrolled in a part-time automotive mechanical apprenticeship course. Distribution characteristics and the resultant norms are compared to earlier normative data reported in the literature and the test manual. The present sample was similar to the preliminary normative group in field-dependence/independence. A number of questions are raised regarding theoretical assumptions underlying current use of the test.

Comparison of Clinical Symptoms and Severity of Sleep Disordered Breathing in Children With and Without Cleft Lip and/or Palate

OBJECTIVE

To determine whether the clinical presentation or severity of sleep disordered breathing differs between children with or without a history of cleft lip and/or palate (CL/P) presenting for sleep assessment.

DESIGN

Retrospective chart review.

SETTING

Tertiary care pediatric hospital cleft clinic, sleep clinic.

PATIENTS

Children >6 months of age presenting to the cleft clinic with sleep concerns and children without CL/P presenting to the sleep clinic in the same 2-year period.

MAIN OUTCOMES MEASURES

Clinical symptoms and overnight polysomnography (PSG) results.

RESULTS

A total of 168 children (55 from cleft clinic, 113 from sleep clinic) were identified. Age at clinical review (6.6 ± 4.1 years versus 6.8 ± 4.0 years, P = ns), sex distribution (64.6% versus 58.4%, P = ns), and the presence of syndromes or significant medical conditions (12% versus 16%, P = ns) were similar between groups. Snoring was the reason for referral in 59% of children with CL/P and 69% of non-CL/P children (P = ns). The only presenting feature that differentiated between the groups was a lower incidence of tonsillar enlargement in children with CL/P (33% versus 79%, chi-square 30.4, P < 0.001). Sleep study results showed similar apnea-hypopnea indices (6.2 ± 6.9 versus 7.9 ± 7.1 events/hr, P = ns) with more central apnea in children with CL/P (1.5 ± 1.5 versus 1.0 ± 1.0 events/hr, P = 0.017).

CONCLUSIONS

Snoring and obstructive sleep apnea are common in CL/P with less tonsillar enlargement than non-CL/P children. Children with CL/P have similar OSA severity compared to non-cleft children but more central apnea which may indicate differences in the control of breathing.

Childhood interstitial lung disease: A systematic review

OBJECTIVES

Childhood interstitial lung disease (chILD) is a group of rare chronic and complex disorders of variable pathology. There has been no systematic review of published chILD research. This study aimed to describe chILD classification systems, epidemiology, morbidity, treatments, outcomes, and the impact of chILD on families and the burden on health services.

METHODS

A systematic literature search for original studies on chILD was undertaken in the major biomedical databases to the end of December 2013. Epidemiological studies, case series and studies describing classification systems were included. Single case studies were excluded.

RESULTS

The search yielded 37 publications that met study criteria. Four different chILD classification systems have been proposed in the past decade. The incidence of chILD has been estimated at 0.13-16.2 cases/100,000 children/year. One to five new cases presented to individual hospitals each year. In developed countries, the median mortality was 13% (6-19%). Morbidity and outcomes were highly variable and not systematically reported. Corticosteroids and hydroxychloroquine were the most common treatments. The impact of chILD on families and the burden on health services has not been studied.

CONCLUSIONS

The heterogeneity of the chILD group of disorders, different determinations of what constitutes a chILD disorder and, a paucity of large epidemiological studies precludes consolidation of results across studies. Consensus on chILD classification is needed to support diagnosis and allow direct comparisons of research evidence. Active disease surveillance and international patient registries are required to advance understanding and management of chILD.

Children's experiences of cystic fibrosis: a systematic review of qualitative studies

BACKGROUND AND OBJECTIVE

Cystic fibrosis (CF) is a common life-shortening genetic disease and is associated with poor psychosocial and quality of life outcomes. The objective of this study was to describe the experiences and perspectives of children and adolescents with CF to direct care toward areas that patients regard as important.

METHODS

MEDLINE, Embase, PsycINFO, and Cumulative Index to Nursing and Allied Health Literature were searched from inception to April 2013. We used thematic synthesis to analyze the findings.

RESULTS

Forty-three articles involving 729 participants aged from 4 to 21 years across 10 countries were included. We identified 6 themes: gaining resilience (accelerated maturity and taking responsibility, acceptance of prognosis, regaining control, redefining normality, social support), lifestyle restriction (limited independence, social isolation, falling behind, physical incapacity), resentment of chronic treatment (disempowerment in health management, unrelenting and exhausting therapy, inescapable illness), temporal limitations (taking risks, setting achievable goals, valuing time), emotional vulnerability (being a burden, heightened self-consciousness, financial strain, losing ground, overwhelmed by transition), and transplant expectations and uncertainty (confirmation of disease severity, consequential timeliness, hope and optimism).

CONCLUSIONS

Adolescents and children with CF report a sense of vulnerability, loss of independence and opportunities, isolation, and disempowerment. This reinforces the importance of the current model of multidisciplinary patient-centered care that promotes shared decision-making, control and self-efficacy in treatment management, educational and vocational opportunities, and physical and social functioning, which can lead to optimal treatment, health, and quality of life outcomes.

Childhood interstitial lung disease due to surfactant protein C deficiency: frequent use and costs of hospital services for a single case in Australia

BACKGROUND

Rare chronic diseases of childhood are often complex and associated with multiple health issues. Such conditions present significant demands on health services, but the degree of these demands is seldom reported. This study details the utilisation of hospital services and associated costs in a single case of surfactant protein C deficiency, an example of childhood interstitial lung disease.

METHODS

Hospital records and case notes for a single patient were reviewed. Costs associated with inpatient services were extracted from a paediatric hospital database. Actual costs were compared to cost estimates based on both disease/procedure-related cost averages for inpatient hospital episodes and a recently implemented Australian hospital funding algorithm (activity-based funding).

RESULTS

To age 8 years and 10 months the child was a hospital inpatient for 443 days over 32 admissions. A total of 298 days were spent in paediatric intensive care. Investigations included 58 chest x-rays, 9 bronchoscopies, 10 lung function tests and 11 sleep studies. Comprehensive disease management failed to prevent respiratory decline and a lung transplant was required. Costs of inpatient care at three tertiary hospitals totalled $966,531 (Australian dollars). Disease- and procedure-related cost averages underestimated costs of paediatric inpatient services for this patient by 68%. An activity-based funding algorithm that is currently being adopted in Australia estimated the cost of hospital health service provision with more accuracy.

CONCLUSIONS

Health service usage and inpatient costs for this case of rare chronic childhood respiratory disease were substantial. This case study demonstrates that disease- and procedure-related cost averages are insufficient to estimate costs associated with rare chronic diseases that require complex management. This indicates that the health service use for similar episodes of hospital care is greater for children with rare diseases than other children. The impacts of rare chronic childhood diseases should be considered when planning resources for paediatric health services.

Effect of general anesthesia on pulmonary function and clinical status on children with cystic fibrosis

INTRODUCTION

Children with cystic fibrosis (CF) receive general anesthesia (GA) for a variety of different procedures. Historical studies assessing risk of GA report a high risk of morbidity. There is a paucity of data evaluating the risk of currently available anesthetic agents. The aim of this study was to assess the effect of GA on clinical status and lung function on children with CF.

METHODS

Children with CF aged 8-18 years admitted for IV antibiotic treatment for a pulmonary exacerbation were invited to participate. Spirometry, forced oscillation technique (FOT), and CF clinical score (CFCS) were measured pre-GA, at 24 and 48 h post-GA. The nature and duration of the GA were recorded.

RESULTS

Twenty two patients were recruited of which 19 patients (mean age 11.4 years, range 8-18 years, 12 male) required GA. Typically, either propofol or sevoflurane was used as induction agent and maintenance of anesthesia was with sevoflurane. A laryngeal mask was used in most cases. FEV1 mean (±SD) pre-GA was 75.1% (±23.46) which decreased at 24 h to 74.8 (±23.0) and at 48 h to 74.3 (±20.5). FOT resistance and reactance decreased at 24 and 48 h from baseline. Changes in spirometry and CFCS were not statistically significant. Two adverse events were observed in this cohort.

CONCLUSION

The results suggest that children with mild to moderate CF lung disease do not experience significant deterioration in central or peripheral airway function following GA. The low rate of complications suggests an improved level of safety for children with CF with modern anesthesia compared with historical published data.

Lower body reaction testing using ultrasonic motion capture

This paper presents a lower body reaction test that utilizes a new portable ultra-sound based motion capture system (MobiFit) combined with a synchronized visual stimulus. This novel system was tested first for criterion validity and agreement against a gold standard laboratory based optical motion capture system (CODA). It was subsequently tested in the field during Gaelic football (GAA) team gym sessions with 35 subjects to demonstrate its utility and versatility. The lower body reaction test itself is novel in that it can be applied to a gross motor task. During testing, participants had sensors attached to their lower limbs and trunk. The speed of movement for each sensor was monitored at 500Hz using the Mobifit motion capture system, and reaction time was measured as the elapsed time from the appearance of a green indicator on the screen to a sensor reaching a set threshold velocity as the participant raised the corresponding leg. Pearson's correlation coefficient tested criterion validity against the CODA system and Intra class correlation coefficients and Bland-Altman plots assessed agreement of velocity measures obtained from the MobiFit and CODA systems. Results indicate that the MobiFit system is an accurate device to assess lower body reaction time and has advantage over standard laboratory measures in terms of portability and ease of set-up.

Consensus statement on standard of care for congenital myopathies

Recent progress in scientific research has facilitated accurate genetic and neuropathological diagnosis of congenital myopathies. However, given their relatively low incidence, congenital myopathies remain unfamiliar to the majority of care providers, and the levels of patient care are extremely variable. This consensus statement aims to provide care guidelines for congenital myopathies. The International Standard of Care Committee for Congenital Myopathies worked through frequent e-mail correspondences, periodic conference calls, 2 rounds of online surveys, and a 3-day workshop to achieve a consensus for diagnostic and clinical care recommendations. The committee includes 59 members from 10 medical disciplines. They are organized into 5 working groups: genetics/diagnosis, neurology, pulmonology, gastroenterology/nutrition/speech/oral care, and orthopedics/rehabilitation. In each care area the authors summarize the committee's recommendations for symptom assessments and therapeutic interventions. It is the committee's goal that through these recommendations, patients with congenital myopathies will receive optimal care and improve their disease outcome.