Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders

Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes. Herein we show the importance of 3 prime untranslated region (3'UTR) non-coding regulatory variants across neurodevelopmental and neuropsychiatric disorders. We devised a pipeline for identifying and functionally validating putatively pathogenic variants from next generation sequencing (NGS) data. We applied this pipeline to a cohort of children with severe specific language impairment (SLI) and identified a functional, SLI-associated variant affecting gene regulation in cells and post-mortem human brain. This variant and the affected gene (ARHGEF39) represent new putative risk factors for SLI. Furthermore, we identified 3'UTR regulatory variants across autism, schizophrenia and bipolar disorder NGS cohorts demonstrating their impact on neurodevelopmental and neuropsychiatric disorders. Our findings show the importance of investigating non-coding regulatory variants when determining risk factors contributing to neurodevelopmental and neuropsychiatric disorders. In the future, integration of such regulatory variation with protein coding changes will be essential for uncovering the genetic causes of complex neurological disorders and the fundamental mechanisms underlying health and disease.

Pooling sputum samples to improve the feasibility of Xpert® MTB/RIF in systematic screening for tuberculosis

SETTING

Systematic screening for tuberculosis (TB) using Xpert® MTB/RIF.

OBJECTIVE

To determine whether pooling sputum samples for Xpert testing may improve the feasibility and cost-effectiveness of Xpert by reducing the number of Xpert tests required.

DESIGN

Mycobacterium tuberculosis-spiked sputum samples at low organism concentrations were used to mimic samples that are more likely to be found in the screening, compared to the diagnostic, setting. Using Xpert, pooled sputum samples were tested from a pooling ratio of 1 in 2 to 1 in 12.

RESULTS

A linear relationship between the pooling ratio and the Xpert MTB cycle threshold (Ct) value was found. As the sputum pooling ratio increased, the Ct value also increased. However, the slope of this increase was relatively small. In the majority of the samples pooled (75/96, 78.1%), Xpert was able to detect M. tuberculosis.

CONCLUSION

These findings suggest that sputum pooling may be a viable method of improving the feasibility and cost-effectiveness of large-scale sputum testing using Xpert in the TB screening setting.

John J, Strauss T, Szelc AM, Tagg N, Terao K, Thomson M, Toups M, Tsai YT, Tufanli S, Usher T, Van De Pontseele W, Van de Water RG, Viren B, Weber M, Wickremasinghe DA, Wolbers S, Wongjirad T, Woodruff K, Yang T, Yates L, Zeller GP, Zennamo J, Zhang C. The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.

A study of human neutrophil antigen genotype frequencies in Hong Kong

BACKGROUND

Alloantibodies against human neutrophil antigens (HNA) are associated with a variety of clinical conditions. Over the past decade, the allelic and genotypic frequencies of the five HNA systems have been evaluated. Although the HNA system is less polymorphic than human leukocyte antigens (HLA), significant differences in the genotypic and allele frequencies still exist in different populations, even those living in close proximity.

OBJECTIVES

To delineate HNA genotypic and allele frequencies to provide vital information on estimating the risk of HNA-associated diseases for our local population.

METHODS

Using a validated, in-house-developed assay, genotyping for HNA-1, HNA-3, HLA-4 and HNA-5 was performed on 300 samples from Chinese blood donors from Hong Kong. In addition, the frequency of the HNA-2 c.843A > T allele was also determined.

RESULTS

The allele frequencies of HNA-1a, -1b and -1c alleles were 67·8, 31·5 and 0%, respectively, whereas the frequencies of HNA-3a and HNA-3b were 71·0 and 29·0%, respectively. The frequencies of HNA-4a and -4b alleles were 99·5 and 0·5%, respectively, and for HNA-5a and -5b, alleles were 85·2 and 14·8%, respectively. Homozygotes for the HNA-2 c.843 TT variant were absent in our population, whereas only <4% of the population were c.843AT heterozygote carriers.

CONCLUSIONS

This is the first study to define HNA genotype and allele frequencies using a validated modified in-house PCR-SSP method in the Hong Kong Chinese blood donor population. Our approach provides a cost-effective assay for conducting routine HNA typing and facilitates the incorporation of these assays into routine clinical service. Our results are comparable with those reported in the Guangzhou Chinese population, but the allele frequencies in our Hong Kong Chinese population are significantly different from the reported European frequencies, confirming that a geographical difference exists for HNA allele frequencies.

The neurocognitive effects of a conducted electrical weapon compared to high intensity interval training and alcohol intoxication - implications for Miranda and consent

While the physiologic effects of conducted electrical weapons (CEW) have been the subjects of numerous studies over nearly two decades, their effects on neurocognitive functioning, both short-term and long-term, have only recently been studied. In a 2014 study involving use-of-force scenarios, including a CEW scenario, we found that there was a decline in neurocognitive performance immediately post-scenario in all groups; however this effect was transient, of questionable clinical/legal significance, not statistically different between the groups, and, returned to baseline by one hour post-scenario. Two subsequent studies by other authors have also found transient neurocognitive effects in the immediate post-exposure period; however, in one study, the effect was greater in one measure (of 5) for the CEW compared to exertion, and the authors suggested that this effect could have implications for the Miranda waiver obtained before custodial interrogation as well as consent. In our current study, we compared the neurocognitive effects of an exposure to a CEW to another exertion regimen, as well as to alcohol intoxication given the latter has significant established case law with regard to the Miranda waiver and consent. Such a comparison may offer more insight into the clinical/legal significance of any measured changes. As with the prior studies, the neurocognitive performance decrements of the CEW and exertion regimens, found only in one measure in this study (of three), were transient, and here, non-significant. Only alcohol intoxication resulted in statistically significant performance declines across all measures and these were persistent over the study period. Given that the neurocognitive changes associated with the CEW were non-significant, but were significant for alcohol intoxication, and given that current case law does not use intoxication as a per se or bright line barrier to Miranda and consent, our results do not suggest that a CEW exposure should preclude waiving of Miranda rights or obtaining consent.

Periostin as a marker of mucosal remodelling in chronic rhinosinusitis

BACKGROUND

Although extracellular matrix (ECM) proteins are associated with irreversible lower airway changes, the relationship with upper airway remodelling which occurs during chronic rhinosinusitis (CRS) is poorly understood. This study assessed the expression of ECM proteins periostin, fibulin-1, fibronectin and collagenIV in nasal mucosa of patients with and without histologic features of remodelling.

METHODS

A cross-sectional study of sinonasal mucosal biopsies taken from patients, undergoing surgery for CRS was performed, where patients were grouped according to remodelling, defined by basement membrane thickening (BMT over 7.5 micrometer) and subepithelial fibrosis. An overall view and three random fields of immunostained tissue sections that included epithelium, basement membrane and submucosa, were imaged using Zeiss Zen software. The area and intensity of positive staining were scored by two blinded observers, using a 12-point ordinal scale of weak to strong.

RESULTS

65 patients (47.6 +/- 13.4years, 44.6% female) were assessed. Patients were grouped as controls 26.2%, BMT/no fibrosis 38.5% or BMT and fibrosis 33.8%. Stronger grade of periostin expression was associated with remodelling changes and tissue eosinophilia over 10/HPF. Fibulin-1, fibronectin and collagenIV did not differ.

CONCLUSION

Periostin expression was associated with the presence of BMT, fibrosis and tissue eosinophilia and may identify patients undergoing remodelling changes.

Periostin as a marker of mucosal remodelling in chronic rhinosinusitis

BACKGROUND

Although extracellular matrix (ECM) proteins are associated with irreversible lower airway changes, the relationship with upper airway remodelling which occurs during chronic rhinosinusitis (CRS) is poorly understood. This study assessed the expression of ECM proteins periostin, fibulin-1, fibronectin and collagenIV in nasal mucosa of patients with and without histologic features of remodelling.

METHODS

A cross-sectional study of sinonasal mucosal biopsies taken from patients, undergoing surgery for CRS was performed, where patients were grouped according to remodelling, defined by basement membrane thickening (BMT over 7.5 micrometer) and subepithelial fibrosis. An overall view and three random fields of immunostained tissue sections that included epithelium, basement membrane and submucosa, were imaged using Zeiss Zen software. The area and intensity of positive staining were scored by two blinded observers, using a 12-point ordinal scale of weak to strong.

RESULTS

65 patients (47.6 +/- 13.4years, 44.6% female) were assessed. Patients were grouped as controls 26.2%, BMT/no fibrosis 38.5% or BMT and fibrosis 33.8%. Stronger grade of periostin expression was associated with remodelling changes and tissue eosinophilia over 10/HPF. Fibulin-1, fibronectin and collagenIV did not differ.

CONCLUSION

Periostin expression was associated with the presence of BMT, fibrosis and tissue eosinophilia and may identify patients undergoing remodelling changes.

Effect of Lung Transplantation on Health-Related Quality of Life in the Era of the Lung Allocation Score: A U.S. Prospective Cohort Study

Under the U.S. Lung Allocation Score (LAS) system, older and sicker patients are prioritized for lung transplantation (LT). The impact of these changes on health-related quality of life (HRQL) after transplant has not been determined. In a single-center prospective cohort study from 2010 to 2016, we assessed HRQL before and repeatedly after LT for up to 3 years using the SF12-Physical and Mental Health, the respiratory-specific Airway Questionnaire 20-Revised, and the Euroqol 5D/Visual Analog Scale utility measures by multivariate linear mixed models jointly modeled with death. We also tested changes in LT-Valued Life Activities disability, BMI, allograft function, and 6-min walk test exercise capacity as predictors of HRQL change. Among 211 initial participants (92% of those eligible), LT improved HRQL by all 5 measures (p < 0.05) and all but SF12-Mental Health improved by threefold or greater than the minimally clinically important difference. Compared to younger participants, those aged ≥65 improved less in SF12-Physical and Mental Health (p < 0.01). Improvements in disability accounted for much of the HRQL improvement. In the LAS era, LT affords meaningful and durable HRQL improvements, mediated by amelioration of disability. Identifying factors limiting HRQL improvement in selected subgroups, especially those aged ≥65, are needed to maximize the net benefits of LT.

Evaluation of C1q Status and Titer of De Novo Donor-Specific Antibodies as Predictors of Allograft Survival

De novo donor-specific antibodies (dnDSAs) that develop after renal transplantation are independent predictors of allograft loss. However, it is unknown if dnDSA C1q status or titer at the time of first detection can independently predict allograft loss. In a consecutive cohort of 508 renal transplant recipients, 70 developed dnDSAs. Histologic and clinical outcomes were correlated with the C1q assay or dnDSA titer. C1q positivity correlated with dnDSA titer (p < 0.01) and mean fluorescence intensity (p < 0.01) and was more common in class II versus class I dnDSAs (p < 0.01). C1q status correlated with tubulitis (p = 0.02) and C4d status (p = 0.03) in biopsies at the time of dnDSA development, but not T cell-mediated rejection (TCMR) or antibody-mediated rejection (ABMR). De novo DSA titer correlated with Banff g, i, t, ptc, C4d scores, TCMR (p < 0.01) and ABMR (p < 0.01). Post-dnDSA graft loss was observed more frequently in recipients with C1q-positve dnDSA (p < 0.01) or dnDSA titer ≥ 1:1024 (p ≤ 0.01). However, after adjustment for clinical phenotype and nonadherence in multivariate models, neither C1q status nor dnDSA titer were independently associated with allograft loss, questioning the utility of these assays at the time of dnDSA development.

The role of macroscopic sputum quality assessments to optimise sputum testing for tuberculosis

SETTING

Community-wide active case finding for tuberculosis (TB) using Xpert® MTB/RIF as the primary screening tool, Ca Mau Province, Viet Nam.

OBJECTIVES

To determine whether macroscopic sputum quality characteristics (sputum colour and volume) can be used to predict Xpert MTB-negative sputum and hence exclude sputum samples from testing.

DESIGN

Field staff conducted household visits to approximately 51,200 adults in 58 villages randomly selected from throughout the province. Sputum samples from all screened participants who were able to produce ⩾1 ml sputum underwent macroscopic sputum assessment and were tested with Xpert.

RESULTS

Of the 21,624 sputum samples tested, 159 (0.74%) were Xpert MTB-positive; 93% of the samples were 1-2 ml and nearly all were mucoid (93%) or mucopurulent (5.7%). One salivary sample was Xpert MTB-positive (2.0% of all salivary samples). The lowest positive predictive value for any sputum volume or colour characteristic was 0.66%. This was not substantially different from the overall prevalence of positive sputum Xpert MTB (0.74%).

CONCLUSION

Sputum colour and volume cannot be used to predict the presence or absence of M. tuberculosis in sputum detected using Xpert. These sputum quality parameters cannot therefore be used to exclude sputum samples from testing for TB.

Importance of papillary muscle infarction detected by cardiac magnetic resonance imaging in predicting cardiovascular events

BACKGROUND

Recent studies suggest that papillary muscle infarction (PMI) following recent myocardial infarction (MI) correlates with adverse cardiovascular outcomes. The purpose of this study is to determine the prevalence and prognostic significance of PMI by cardiac magnetic resonance (CMR) in a large cohort of patients.

METHODS

Retrospective study of patients who underwent CMR between January 2007 and December 2009 were evaluated for the presence of PMI in one or both of the left ventricle papillary muscles. The primary outcome was a time to a combined endpoint of all-cause mortality and worsening heart failure. Secondary outcomes were time to individual components of the combined outcome.

RESULTS

419 patients were included in our analysis, 232 patients (55%) had ischemic cardiomyopathy. Patients were followed at six-month intervals for a median follow-up time of 3.7 (interquartile range (IQR): 1.6; 6.3) years after initial imaging. During this period 196 patients (46.8%) had a primary outcome and 92 patients (22%) died. PM infarct was identified in 204 (48.7%) patients with twice as many posteromedial (PRM) (27%) than anterolateral (ARL) lesions (11%) and a similar number with infarct in both (11%). There was no association between studied outcomes and the presence of PMI in either PRM or ARL PM. The presence of infarct in both PM was a predictor of both the primary outcome (HR 1.69, CI[1.01-2.86], p<0.049.) and mortality (HR 1.69, CI[1.01-4.2], p<0.046).

CONCLUSION

The presence of infarct in either papillary muscle was not associated with outcomes. However, infarct involving both papillary muscles was associated with worse outcomes.