Detection of Mycobacterium tuberculosis in human tissue via RNA in situ hybridization

Rationale

Accurate TB diagnosis is hampered by the variable efficacy of the widely-used Ziehl-Neelsen (ZN) staining method to identify Mycobacterium tuberculosis ( Mtb ) acid-fast bacilli (AFB). Here, we sought to circumvent this current limitation through direct detection of Mtb mRNA.

Objectives

To employ RNAscope to determine the spatial distribution of Mtb mRNA within tuberculous human tissue, to appraise ZN-negative tissue from confirmed TB patients, and to provide proof-of-concept of RNAscope as a platform to inform TB diagnosis and Mtb biology.

Methods

We examined ante- and postmortem human TB tissue using RNAscope to detect Mtb mRNA and a dual ZN/immunohistochemistry staining approach to identify AFB and bacilli producing antigen 85B (Ag85B).

Measurements and main results

We adapted RNAscope for Mtb and identified intact and disintegrated Mtb bacilli and intra- and extracellular Mtb mRNA. Mtb mRNA was distributed zonally within necrotic and non-necrotic granulomas. We also found Mtb mRNA within, and adjacent to, necrotic granulomas in ZN-negative lung tissue and in Ag85B-positive bronchial epithelium. Intriguingly, we observed accumulation of Mtb mRNA and Ag85B in the cytoplasm of host cells. Notably, many AFB were negative for Ag85B staining. Mtb mRNA was observed in ZN-negative antemortem lymph node biopsies.

Conclusions

RNAscope has diagnostic potential and can guide therapeutic intervention as it detects Mtb mRNA and morphology in ZN-negative tissues from TB patients, and Mtb mRNA in ZN-negative antemortem biopsies, respectively. Lastly, our data provide evidence that at least two phenotypically distinct populations of Mtb bacilli exist in vivo .

Polygenic Risk Score in African populations: progress and challenges

Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects  single nucleotide polymorphisms (SNPs) that  contribute to the disease with low effect size  making it more precise at individual level risk prediction. PRS  analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with  low effect size but play an indispensable role to the observed phenotypic/trait variance.  PRS analysis has  applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies  show   that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that  lack of sufficient GWAS data and tools is  the limiting factor of applying PRS analysis to sub-Saharan populations.   We recommend developing Africa-specific PRS methods and tools for estimating and analyzing  African population data   for clinical  evaluation of PRSs of interest and predicting  rare diseases.

Polygenic Risk Score in African populations: progress and challenges

Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects  single nucleotide polymorphisms (SNPs) that  contribute to the disease with low effect size  making it more precise at individual level risk prediction. PRS  analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with  low effect size but play an indispensable role to the observed phenotypic/trait variance.  PRS analysis has  applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies  show   that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that  lack of sufficient GWAS data and tools is  the limiting factor of applying PRS analysis to sub-Saharan populations.   We recommend developing Africa-specific PRS methods and tools for estimating and analyzing  African population data   for clinical  evaluation of PRSs of interest and predicting  rare diseases.

A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions

Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.

A Short Report Examining the Introduction of Routine Use of Patient-Reported Outcome Measures in a Mixed Oncology Population

AIMS

People living with treatable but not curable cancer often experience a range of symptoms related to their cancer and its treatment. During the COVID-19 pandemic, face-to-face consultations were reduced and so remote monitoring of these needs was necessary. University Hospitals Sussex implemented the routine use of electronic remote patient-reported outcome measures (PROMs) in a mixed oncology population, focusing on those with treatable but not curable cancers.

MATERIALS AND METHODS

Over a 9-month period, patients were invited to register with My Clinical Outcomes (MCO) - a secure online platform for the collection of electronic PROMs. They were prompted by e-mail to complete assessments (EORTC QLQ-C30, EQ-5D-3L and EQ-5D VAS) routinely every 2 weeks. The team monitored patient scores and changes in these prompted clinical interventions.

RESULTS

In total, 324 patients completed at least one assessment. The median number of assessments completed by each patient was eight. The most represented tumour groups were secondary breast (28%), prostate (25%) and other (32%). Median scores for the assessments did not deteriorate in a clinically or numerically significant way for patients living with non-curable conditions for the majority of patients monitored.

CONCLUSION

Routine collection of electronic remote PROMs is an effective and useful strategy to provide real-time clinical feedback to teams. With integration into existing systems, online platforms (such as MCO) could provide efficient and patient-centred information for those providing care for people with cancer.

Micro-Computed Tomography Analysis of the Human Tuberculous Lung Reveals Remarkable Heterogeneity in Three-dimensional Granuloma Morphology

Rationale: Our current understanding of tuberculosis (TB) pathophysiology is limited by a reliance on animal models, the paucity of human TB lung tissue, and traditional histopathological analysis, a destructive two-dimensional approach that provides limited spatial insight. Determining the three-dimensional (3D) structure of the necrotic granuloma, a characteristic feature of TB, will more accurately inform preventive TB strategies.Objectives: To ascertain the 3D shape of the human tuberculous granuloma and its spatial relationship with airways and vasculature within large lung tissues.Methods: We characterized the 3D microanatomical environment of human tuberculous lungs by using micro computed tomography, histopathology, and immunohistochemistry. By using 3D segmentation software, we accurately reconstructed TB granulomas, vasculature, and airways in three dimensions and confirmed our findings by using histopathology and immunohistochemistry.Measurements and Main Results: We observed marked heterogeneity in the morphology, volume, and number of TB granulomas in human lung sections. Unlike depictions of granulomas as simple spherical structures, human necrotic granulomas exhibit complex, cylindrical, branched morphologies that are connected to the airways and shaped by the bronchi. The use of 3D imaging of human TB lung sections provides unanticipated insight into the spatial organization of TB granulomas in relation to the airways and vasculature.Conclusions: Our findings highlight the likelihood that a single, structurally complex lesion could be mistakenly viewed as multiple independent lesions when evaluated in two dimensions. In addition, the lack of vascularization within obstructed bronchi establishes a paradigm for antimycobacterial drug tolerance. Lastly, our results suggest that bronchogenic spread of Mycobacterium tuberculosis reseeds the lung.

Author Correction: High-depth African genomes inform human migration and health

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03286-9.

Early COVID-19 Pandemic Modeling: Three Compartmental Model Case Studies From Texas, USA

The novel coronavirus (SARS-CoV-2) emerged in late 2019 and spread globally in early 2020. Initial reports suggested the associated disease, COVID-19, produced rapid epidemic growth and caused high mortality. As the virus sparked local epidemics in new communities, health systems and policy makers were forced to make decisions with limited information about the spread of the disease. We developed a compartmental model to project COVID-19 healthcare demands that combined information regarding SARS-CoV-2 transmission dynamics from international reports with local COVID-19 hospital census data to support response efforts in three metropolitan statistical areas in Texas, USA: Austin-Round Rock, Houston-The Woodlands-Sugar Land, and Beaumont-Port Arthur. Our model projects that strict stay-home orders and other social distancing measures could suppress the spread of the pandemic. Our capacity to provide rapid decision-support in response to emerging threats depends on access to data, validated modeling approaches, careful uncertainty quantification, and adequate computational resources.

High-depth African genomes inform human migration and health

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed¹. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

Compromised Metabolic Reprogramming Is an Early Indicator of CD8+ T Cell Dysfunction during Chronic Mycobacterium tuberculosis Infection

The immunometabolic mechanisms underlying suboptimal T cell immunity in tuberculosis remain undefined. Here, we examine how chronic Mycobacterium tuberculosis (Mtb) and M. bovis BCG infections rewire metabolic circuits and alter effector functions in lung CD8⁺ T cells. As Mtb infection progresses, mitochondrial metabolism deteriorates in CD8⁺ T cells, resulting in an increased dependency on glycolysis that potentiates inflammatory cytokine production. Over time, these cells develop bioenergetic deficiencies that reflect metabolic “quiescence.” This bioenergetic signature coincides with increased mitochondrial dysfunction and inhibitory receptor expression and was not observed in BCG infection. Remarkably, the Mtb-triggered decline in T cell bioenergetics can be reinvigorated by metformin, giving rise to an Mtb-specific CD8⁺ T cell population with improved metabolism. These findings provide insights into Mtb pathogenesis whereby glycolytic reprogramming and compromised mitochondrial function contribute to the breakdown of CD8⁺ T cell immunity during chronic disease, highlighting opportunities to reinvigorate immunity with metabolically targeted pharmacologic agents.

•

T cells from Mtb and BCG infections have unique metabolic and functional signatures

•

Mitochondrial metabolism deteriorates in effector T cells as Mtb infection persists

•

Metformin rejuvenates mitochondrial metabolism in T cells from Mtb-infected mice

•

The breakdown of Mtb immunity during chronic disease is linked to immunometabolism

trips4health: Protocol of a single-blinded randomised controlled trial incentivising adults to use public transport for physical activity gain

Background

Public transport (PT) users typically accumulate more physical activity (PA) than private motor vehicle users yet redressing physical inactivity through transport-related PA (TRPA) interventions has received limited attention. Further, incentive-based strategies can increase leisure-time PA but their impact on TRPA, is unclear. This study's objective is to determine the impact of an incentive-based strategy on TRPA in a regional Australian setting.

Methods

trips4health is a single-blinded randomised controlled trial with a four-month intervention phase and subsequent six-month maintenance phase. Participants will be randomised to: an incentives-based intervention (bus trip credit for reaching bus trip targets, weekly text messages to support greater bus use, written PA guidelines); or an active control (written PA guidelines only). Three hundred and fifty adults (≥18 years) from southern Tasmania will be recruited through convenience methods, provide informed consent and baseline information, then be randomised. The primary outcome is change in accelerometer measured average daily step count at baseline and four- and ten-months later. Secondary outcomes are changes in: measured and self-reported travel behaviour (e.g. PT use), PA, sedentary behaviour; self-reported and measured (blood pressure, waist circumference, height, weight) health; travel behaviour perspectives (e.g. enablers/barriers); quality of life; and transport-related costs. Linear mixed model regression will determine group differences. Participant and PT provider level process evaluations will be conducted and intervention costs to the provider determined.

Discussion

trips4health will determine the effectiveness of an incentive-based strategy to increase TRPA by targeting PT use. The findings will enable evidence-informed decisions about the worthwhileness of such strategies.

Trial registration

ACTRN12619001136190.

Universal trial number

U1111-1233-8050.

THU0614-HPR ASSESSING THE EFFECT OF INTERVENTIONS FOR AXIAL SPONDYLOARTHRITIS ACCORDING TO THE ENDORSED ASAS/OMERACT CORE OUTCOME SET: A META-RESEARCH STUDY OF TRIALS INCLUDED IN COCHRANE REVIEWS

Background:

The Assessment of SpondyloArthritis international Society (ASAS) has defined separate core sets for: i) symptom-modifying anti-rheumatic drugs (SM-ARD), ii) clinical record keeping, and iii) disease-controlling anti-rheumatic therapy (DC-ART). These all include the following domains: ‘physical function’, ‘pain’, ‘spinal mobility’, ‘spinal stiffness’ and ‘patient global assessment’ (PGA). The core set for clinical record keeping further includes the domains ‘peripheral joints’ and ‘acute phase reactants’, and the core set for DC-ART further includes the domains ‘fatigue’, ‘spine/hip radiographs’.

Objectives:

To assess the effect of interventions for each of the 9 axSpA core domains.

Methods:

We investigated the efficacy across all interventions included in Cochrane reviews according to the core outcome set for axSpA, as reported in these eligible axSpA trials. We combined data using the standardized mean difference (SMD) to meta-analyze outcomes involving similar constructs. By meta-regression analysis, we examined the effect for each of the nine separate SMD measures on the primary endpoint across all trials.

Results:

Among 85 articles screened, we included 43 trials with 63 randomized comparisons. Mean (SD) number of core outcomes domains measured for SM-ARD trials was 4.2 (1.7). 6 trials assessed all 5 proposed domains. Mean (SD) for number of core outcome domains for DC-ART trials was 5.8 (1.7). Unfortunately, no trials assessed all 9 domains. 8 trials were judged to have high risk of selective outcome reporting. The most responsible core domains for achieving success in meeting the primary objective per trial were pain; OR (95% CI) 5.19 (2.28, 11.77) and PGA; OR (95% CI) 1.87 (1.14, 3.07).

Conclusion:

Overall outcome reporting was good for SM-ARD trials, and poor for DC-ART trials. None of the DC-ART trials assessed all 9 domains. Outcome-reporting bias and ‘missing data’ should be reduced by implementing the endorsed ASAS/OMERACT outcome domains in all clinical trials. Our findings suggest that PGA and pain likely provide a holistic assessment of disease beyond “objective measures” of spinal inflammation.

Disclosure of Interests:

Rikke Asmussen Andreasen: None declared, Lars Erik Kristensen Consultant of: UCB Pharma (Advisory Board), Sannofi (Advisory Board), Abbvie (Advisory Board), Biogen (Advisory Board), Speakers bureau: AbbVie, Amgen, Biogen, Bristol-Myers Squibb,Celgene, Eli Lilly, Gilead, Forward Pharma, Janssen Pharmaceuticals, MSD, Novartis, Pfizer, and UCB Pharma, Xenofon Baraliakos Grant/research support from: Grant/research support from: AbbVie, BMS, Celgene, Chugai, Merck, Novartis, Pfizer, UCB and Werfen, Consultant of: AbbVie, BMS, Celgene, Chugai, Merck, Novartis, Pfizer, UCB and Werfen, Speakers bureau: AbbVie, BMS, Celgene, Chugai, Merck, Novartis, Pfizer, UCB and Werfen, Vibeke Strand Consultant of: AbbVie, Amgen, Biogen, Celltrion, Consortium of Rheumatology Researchers of North America, Crescendo Bioscience, Eli Lilly, Genentech/Roche, GlaxoSmithKline, Hospira, Janssen, Merck, Novartis, Pfizer, Regeneron Pharmaceuticals, Inc., Sanofi, UCB, Philip J Mease Grant/research support from: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – grant/research support, Consultant of: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – consultant, Speakers bureau: Abbott, Amgen, Biogen Idec, BMS, Eli Lilly, Genentech, Janssen, Pfizer, UCB – speakers bureau, Maarten de Wit Grant/research support from: Dr. de Wit reports personal fees from Ely Lilly, 2019, personal fees from Celgene, 2019, personal fees from Pfizer, 2019, personal fees from Janssen-Cilag, 2017, outside the submitted work., Consultant of: Dr. de Wit reports personal fees from Ely Lilly, 2019, personal fees from Celgene, 2019, personal fees from Pfizer, 2019, personal fees from Janssen-Cilag, 2017, outside the submitted work., Speakers bureau: Dr. de Wit reports personal fees from Ely Lilly, 2019, personal fees from Celgene, 2019, personal fees from Pfizer, 2019, personal fees from Janssen-Cilag, 2017, outside the submitted work., Torkell Ellingsen: None declared, Inger Marie Jensen Hansen: None declared, Jamie Kirkham: None declared, George Wells: None declared, Peter Tugwell: None declared, Lara Maxwell: None declared, Maarten Boers: None declared, Kenneth Egstrup: None declared, Robin Christensen Grant/research support from: Dr. Christensen reports non-financial support from Board membership, grants from Consultancy (AbbVie, Amgen, Axellus A/S, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Eli Lilly, Hospira, MSD, Norpharma, Novartis, Orkla Health, Pfizer, Roche, Sobi, Takeda), personal fees from Employment (Research Unit for Musculoskeletal Function and Physiotherapy, Institute of Sports Science and Clinical Biomechanics, University of Southern Denmark), non-financial support from Expert testimony, grants from Grants/grants pending (Axellus A/S, AbbVie, Cambridge Weight Plan, Janssen, MSD, Mundipharma, Novartis, and Roche), grants from Payment for lectures including service on speakers bureaus (Abbott, Amgen, Axellus, Bayer HealthCare Pharmaceuticals, Biogen Idec, Bristol-Myers Squibb, Cambridge Weight Plan, Ipsen, Janssen, Laboratoires Expanscience, MSD, Mundipharma, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, Sobi, and Wyeth), grants from Payment for manuscript preparation (Axellus, Bristol-Myers Squibb, and Cambridge Weight Plan, Aleris-Hamlet (via Norpharma)), non-financial support from Patents (planned, pending or issued), non-financial support from Royalties, grants from Payment for development of educational presentations (Bristol-Myers Squibb, MSD, Pfizer), non-financial support from Stock/stock options, grants from Travel/accommodations/meeting expenses unrelated to activities listed (Abbott, AbbVie, Axellus, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Laboratoires Expanscience, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, and Wyeth), non-financial support from Other (err on the side of full disclosure), outside the submitted work; and I am involved in many health-care initiatives and research that could benefit from wide uptake of this publication (including Cochrane, OMERACT, IDEOM, RADS, and the GRADE Working Group).

Musculoskeletal Statistics Unit, The Parker Institute is grateful for the financial support received from public and private foundations, companies and private individuals over the years. The Parker Institute is supported by a core grant from the Oak Foundation; The Oak Foundation is a group of philanthropic organizations that, since its establishment in 1983, has given grants to not-for-profit organizations around the world.., Consultant of: Dr. Christensen reports non-financial support from Board membership, grants from Consultancy (AbbVie, Amgen, Axellus A/S, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Eli Lilly, Hospira, MSD, Norpharma, Novartis, Orkla Health, Pfizer, Roche, Sobi, Takeda), personal fees from Employment (Research Unit for Musculoskeletal Function and Physiotherapy, Institute of Sports Science and Clinical Biomechanics, University of Southern Denmark), non-financial support from Expert testimony, grants from Grants/grants pending (Axellus A/S, AbbVie, Cambridge Weight Plan, Janssen, MSD, Mundipharma, Novartis, and Roche), grants from Payment for lectures including service on speakers bureaus (Abbott, Amgen, Axellus, Bayer HealthCare Pharmaceuticals, Biogen Idec, Bristol-Myers Squibb, Cambridge Weight Plan, Ipsen, Janssen, Laboratoires Expanscience, MSD, Mundipharma, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, Sobi, and Wyeth), grants from Payment for manuscript preparation (Axellus, Bristol-Myers Squibb, and Cambridge Weight Plan, Aleris-Hamlet (via Norpharma)), non-financial support from Patents (planned, pending or issued), non-financial support from Royalties, grants from Payment for development of educational presentations (Bristol-Myers Squibb, MSD, Pfizer), non-financial support from Stock/stock options, grants from Travel/accommodations/meeting expenses unrelated to activities listed (Abbott, AbbVie, Axellus, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Laboratoires Expanscience, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, and Wyeth), non-financial support from Other (err on the side of full disclosure), outside the submitted work; and I am involved in many health-care initiatives and research that could benefit from wide uptake of this publication (including Cochrane, OMERACT, IDEOM, RADS, and the GRADE Working Group).

Musculoskeletal Statistics Unit, The Parker Institute is grateful for the financial support received from public and private foundations, companies and private individuals over the years. The Parker Institute is supported by a core grant from the Oak Foundation; The Oak Foundation is a group of philanthropic organizations that, since its establishment in 1983, has given grants to not-for-profit organizations around the world.., Speakers bureau: Dr. Christensen reports non-financial support from Board membership, grants from Consultancy (AbbVie, Amgen, Axellus A/S, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Eli Lilly, Hospira, MSD, Norpharma, Novartis, Orkla Health, Pfizer, Roche, Sobi, Takeda), personal fees from Employment (Research Unit for Musculoskeletal Function and Physiotherapy, Institute of Sports Science and Clinical Biomechanics, University of Southern Denmark), non-financial support from Expert testimony, grants from Grants/grants pending (Axellus A/S, AbbVie, Cambridge Weight Plan, Janssen, MSD, Mundipharma, Novartis, and Roche), grants from Payment for lectures including service on speakers bureaus (Abbott, Amgen, Axellus, Bayer HealthCare Pharmaceuticals, Biogen Idec, Bristol-Myers Squibb, Cambridge Weight Plan, Ipsen, Janssen, Laboratoires Expanscience, MSD, Mundipharma, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, Sobi, and Wyeth), grants from Payment for manuscript preparation (Axellus, Bristol-Myers Squibb, and Cambridge Weight Plan, Aleris-Hamlet (via Norpharma)), non-financial support from Patents (planned, pending or issued), non-financial support from Royalties, grants from Payment for development of educational presentations (Bristol-Myers Squibb, MSD, Pfizer), non-financial support from Stock/stock options, grants from Travel/accommodations/meeting expenses unrelated to activities listed (Abbott, AbbVie, Axellus, Biogen, Bristol-Myers Squibb, Cambridge Weight Plan, Celgene, Laboratoires Expanscience, Norpharma, Novartis, Pfizer, Roche, Rottapharm-Madaus, and Wyeth), non-financial support from Other (err on the side of full disclosure), outside the submitted work; and I am involved in many health-care initiatives and research that could benefit from wide uptake of this publication (including Cochrane, OMERACT, IDEOM, RADS, and the GRADE Working Group).

Musculoskeletal Statistics Unit, The Parker Institute is grateful for the financial support received from public and private foundations, companies and private individuals over the years. The Parker Institute is supported by a core grant from the Oak Foundation; The Oak Foundation is a group of philanthropic organizations that, since its establishment in 1983, has given grants to not-for-profit organizations around the world.

Ten simple rules for providing effective bioinformatics research support

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support.

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research

BACKGROUND

Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation.

RESULTS

The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD.

CONCLUSION

To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.

P5604Combining aortic size with measures of aortic stiffness and pulsatile hemodynamics enhances prediction of future thoracic aortic aneurysm expansion

Introduction

Thoracic aortic aneurysm (TAA) is a clinically silent disease which can lead to significant morbidity when complicated by an acute aortic syndrome. Although TAA size is the only variable used in decision-making, it is an imperfect predictor of risk. Conversely, hemodynamic measures that reflect the aorta's function, such as aortic stiffness and pulsatile hemodynamics, may provide additional insights into risk of TAA expansion.

Purpose

We hypothesized that combining aortic size with measures of arterial function (stiffness and pulsatile hemodynamics) would improve prediction of TAA expansion, as compared to aortic size alone.

Methods

105 unoperated participants with TAA were recruited between 2014 and 2017 and followed prospectively for ≥1 yr. TAA size was measured at enrolment and at the latest imaging study according to published consensus; TAA expansion was calculated as mm/year. Arterial function was non-invasively assessed at baseline with validated methods that integrate arterial tonometry with echocardiography. Multivariable linear regression assessed independent associations of baseline TAA size and each arterial function measure, initially separately and then in combination (by multiplying them when direction of association was the same, and dividing them when direction of association was opposite), with future TAA expansion. Standardized beta coefficients were calculated to allow direct comparisons. Models were adjusted for age, sex, body size, aneurysm location and etiology, type of imaging modality, follow-up time, mean arterial pressure, and history of hypertension, diabetes and smoking.

Results

Seventy-seven percent of participants were men, and the ratio of degenerative to heritable TAAs was 62/43. Mean ± SD age, baseline TAA size, and follow-up time were 62.8±11.3yrs, 46.3±3.9cm, and 2.2±0.7 years, respectively. Results of the multivariable linear regression models are summarized in the Table. While baseline TAA size and each arterial function measure were independently associated with TAA expansion, some of the arterial function measures were superior in predicting TAA growth (Table, left). In addition, combining aortic size and function further improved the prediction of TAA growth beyond each variable alone (Table, right).

Conclusion(s)

Combining aortic size with arterial function improved prediction of TAA expansion over any individual variable alone, independently of confounders. Assessing arterial function may confer a clinical advantage, when compared to current practice, in determining TAA disease activity and estimating one's TAA-related risk.

Acknowledgement/Funding

Canadian Institute of Health Research, Canadian Vascular Network, and Heart and Stroke Foundation of Canada

P6546Canadian Registry of Electronic Device Outcomes (CREDO): remote monitoring outcomes in the abbott battery performance alert, a multicentre cohort

Background

Cardiac implantable electronic devices have been known to have lead and device malfunctions leading to advisories. Increased use of remote monitoring of devices has been suggested to allow the identification of abnormal device performance and allow early intervention. We sought to describe the outcomes of patients with and without remote monitoring of in devices in the Abbott Premature Battery Depletion advisory with data from a Canadian registry

Methods

Patients with an Abbott device subject to the Battery Performance Alert Advisory from nine ICD implanting centres in Canada were included in the registry. The use of remote monitoring was identified from baseline and followup data in the registry. The primary outcome was detection of premature battery depletion and all cause mortality.

Results

2679 patents were identified with a device subject to the advisory. Devices were implanted between 2010 and 2017. 1716 patients (64%) had remote monitoring at baseline with this increasing to 83.7% at followup at 12 months. Premature battery depletion occurred in 43 patients (1.6%). Discovery of premature battery depletion was detected by remote monitoring in 70% of patients. There were 492 deaths during the follow up. Mortality was higher in those without a remote monitor compared to those with a remote monitor at follow-up and remote monitor at baseline and follow-up (11.3%, 2.6% versus 6.1% respectively; p=0.0186). There were no deaths attributed to premature battery depletion

Conclusion

The use of remote monitoring in patients with ICD and CRT under advisory reliably detected device failure and was associated with a reduction in all-cause mortality.

Improved diagnostic criteria for digital flexor tendon sheath pathology using contrast tenography

BACKGROUND

Pathology of the digital flexor tendon sheath is a significant cause of lameness in the horse. Imaging is important to identify lesions and inform on prognosis prior to tenoscopic surgery.

OBJECTIVES

To use a large population to evaluate 1) the sensitivity and specificity of digital flexor tendon sheath (DFTS) contrast radiographs in diagnosing manica flexoria (MF) tears, deep digital flexor tendon (DDFT) tears and constriction of the palmar/plantar annular ligament (PAL) using novel criteria; 2) predisposition to pathology in signalment and limb affected.

STUDY DESIGN

Multicentre retrospective cohort study.

METHODS

The medical records of 206 horses with lameness localised to the DFTS, contrast radiographs and subsequent tenoscopic surgery were reviewed. Breed and limb predispositions were evaluated for pathology of the DDFT, MF and PAL constriction. Contrast radiographs of the DFTS were reviewed by four masked operators and for each pathology the sensitivity, specificity and interobserver variability were calculated.

RESULTS

Contrast tenography was a sensitive test for MF tears (92% confidence interval [CI] 88.4-94.4%; specificity 56%, CI 51.1-61.1%) and specific for diagnosing DDFT tears (73%, CI 68.6-76.8%; sensitivity 54%, CI 47.8-60.2%) but had a lower sensitivity (71%, CI 65.1-75.9% ) and specificity (45%, CI 39.1-52.0%) for PAL constriction. It had good to substantial interobserver agreement for MF and DDFT tears (Krippendorff's alpha 0.68 and 0.46 respectively). Ponies (57%) and cobs (58%) were significantly more likely to be affected with MF tears (other breeds 20-39%, P = 0.003) and Thoroughbreds (50%), warmbloods (45%) and draught breeds (48%) were more likely to have DDFT tears (other breeds 22-34%, P = 0.01). MF tears and PAL constriction were overrepresented in the hindlimbs compared to DDFT tears in forelimbs.

MAIN LIMITATIONS

No standardisation of contrast radiographs was possible. The subjectivity of diagnosis of PAL constriction may also have led to bias. Radiographs were read as JPEGS reducing ability to manipulate images.

CONCLUSIONS

Contrast radiography of the DFTS is accurate in the pre-operative diagnosis of DFTS pathologies. Different pathologies are overrepresented in certain breeds and limbs.

Microanatomic Distribution of Myeloid Heme Oxygenase-1 Protects against Free Radical-Mediated Immunopathology in Human Tuberculosis

Heme oxygenase-1 (HO-1) is a cytoprotective enzyme that controls inflammatory responses and redox homeostasis; however, its role during pulmonary tuberculosis (TB) remains unclear. Using freshly resected human TB lung tissue, we examined the role of HO-1 within the cellular and pathological spectrum of TB. Flow cytometry and histopathological analysis of human TB lung tissues showed that HO-1 is expressed primarily in myeloid cells and that HO-1 levels in these cells were directly proportional to cytoprotection. HO-1 mitigates TB pathophysiology by diminishing myeloid cell-mediated oxidative damage caused by reactive oxygen and/or nitrogen intermediates, which control granulocytic karyorrhexis to generate a zonal HO-1 response. Using whole-body or myeloid-specific HO-1-deficient mice, we demonstrate that HO-1 is required to control myeloid cell infiltration and inflammation to protect against TB progression. Overall, this study reveals that zonation of HO-1 in myeloid cells modulates free-radical-mediated stress, which regulates human TB immunopathology.

The GluN2B-Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand-unbinding and domain opening

N-methyl-D-aspartate (NMDA) receptors are transmembrane glutamate-binding ion channels that mediate neurotransmission in mammals. NMDA receptor subunits are tetrameric complexes of GluN1 and GluN2A-D subunits, encoded by the GRIN gene family. Of these subunits, GluN2B is suggested to be required for normal development of the central nervous system. A mutation identified in a patient with developmental delay, E413G, resides in the GluN2B ligand-binding domain and substantially reduces glutamate potency by an unknown mechanism. GluN2B Gly413, though near the agonist, is not in van der Waals contact with glutamate. Visual analysis of the GluN2B structure with the E413G mutation modeled suggests that replacement of Glu with Gly at this position increases solvent access to the ligand-binding domain. This was confirmed by molecular modeling, which showed that the ligand is more mobile in GluN2B-E413G than WT GluN2B. Evaluation of agonist occupancy using random accelerated molecular dynamics (RAMD) simulations predicts that the glutamate exits the binding-site more rapidly for GluN2B-E413G than WT receptors. This analysis was extended to other binding-site mutations, which produced qualitative agreement between experimentally determined EC₅₀ values, deactivation time constants, and ligand motion within the binding-site. Furthermore, long sub-microsecond molecular dynamics simulations of the bi-lobed ligand-binding domain revealed that it adopted a cleft-open ligand-free state more often for GluN2B-E413G than wild-type GluN2B. This is consistent with the idea that L-glutamate binding is altered such that the ligand-binding domain occupies the open-cleft conformation associated with the closed channel.

When is a randomised controlled trial health equity relevant? Development and validation of a conceptual framework

BACKGROUND

Randomised controlled trials can provide evidence relevant to assessing the equity impact of an intervention, but such information is often poorly reported. We describe a conceptual framework to identify health equity-relevant randomised trials with the aim of improving the design and reporting of such trials.

METHODS

An interdisciplinary and international research team engaged in an iterative consensus building process to develop and refine the conceptual framework via face-to-face meetings, teleconferences and email correspondence, including findings from a validation exercise whereby two independent reviewers used the emerging framework to classify a sample of randomised trials.

RESULTS

A randomised trial can usefully be classified as 'health equity relevant' if it assesses the effects of an intervention on the health or its determinants of either individuals or a population who experience ill health due to disadvantage defined across one or more social determinants of health. Health equity-relevant randomised trials can either exclusively focus on a single population or collect data potentially useful for assessing differential effects of the intervention across multiple populations experiencing different levels or types of social disadvantage. Trials that are not classified as 'health equity relevant' may nevertheless provide information that is indirectly relevant to assessing equity impact, including information about individual level variation unrelated to social disadvantage and potentially useful in secondary modelling studies.

CONCLUSION

The conceptual framework may be used to design and report randomised trials. The framework could also be used for other study designs to contribute to the evidence base for improved health equity.

Antiplasmodial Mode of Action of Pantothenamides: Pantothenate Kinase Serves as a Metabolic Activator Not as a Target

N-Substituted pantothenamides (PanAms) are pantothenate analogues with up to nanomolar potency against blood-stage Plasmodium falciparum (the most virulent species responsible for malaria). Although these compounds are known to target coenzyme A (CoA) biosynthesis and/or utilization, their exact mode of action (MoA) is still unknown. Importantly, PanAms that retain the natural β-alanine moiety are more potent than other variants, consistent with the involvement of processes that are selective for pantothenate (the precursor of CoA) or its derivatives. The transport of pantothenate and its phosphorylation by P. falciparum pantothenate kinase (PfPanK, the first enzyme of CoA biosynthesis) are two such processes previously highlighted as potential targets for the PanAms' antiplasmodial action. In this study, we investigated the effect of PanAms on these processes using their radiolabeled versions (synthesized here for the first time), which made possible the direct measurement of PanAm uptake by isolated blood-stage parasites and PanAm phosphorylation by PfPanK present in parasite lysates. We found that the MoA of PanAms does not involve interference with pantothenate transport and that inhibition of PfPanK-mediated pantothenate phosphorylation does not correlate with PanAm antiplasmodial activity. Instead, PanAms that retain the β-alanine moiety were found to be metabolically activated by PfPanK in a selective manner, forming phosphorylated products that likely inhibit other steps in CoA biosynthesis or are transformed into CoA antimetabolites that can interfere with CoA utilization. These findings provide direction for the ongoing development of CoA-targeted inhibitors as antiplasmodial agents with clinical potential.

Mechanistic Insight into NMDA Receptor Dysregulation by Rare Variants in the GluN2A and GluN2B Agonist Binding Domains

Epilepsy and intellectual disability are associated with rare variants in the GluN2A and GluN2B (encoded by GRIN2A and GRIN2B) subunits of the N-methyl-D-aspartate receptor (NMDAR), a ligand-gated ion channel with essential roles in brain development and function. By assessing genetic variation across GluN2 domains, we determined that the agonist binding domain, transmembrane domain, and the linker regions between these domains were particularly intolerant to functional variation. Notably, the agonist binding domain of GluN2B exhibited significantly more variation intolerance than that of GluN2A. To understand the ramifications of missense variation in the agonist binding domain, we investigated the mechanisms by which 25 rare variants in the GluN2A and GluN2B agonist binding domains dysregulated NMDAR activity. When introduced into recombinant human NMDARs, these rare variants identified in individuals with neurologic disease had complex, and sometimes opposing, consequences on agonist binding, channel gating, receptor biogenesis, and forward trafficking. Our approach combined quantitative assessments of these effects to estimate the overall impact on synaptic and non-synaptic NMDAR function. Interestingly, similar neurologic diseases were associated with both gain- and loss-of-function variants in the same gene. Most rare variants in GluN2A were associated with epilepsy, whereas GluN2B variants were associated with intellectual disability with or without seizures. Finally, discerning the mechanisms underlying NMDAR dysregulation by these rare variants allowed investigations of pharmacologic strategies to correct NMDAR function.

Does salmon calcitonin cause cancer? A review and meta-analysis

Recently an association between the use of calcitonin and cancer has been postulated. We reviewed the biological rationale and performed an additional analysis of historical data with respect to the possibility. An association cannot be excluded, but the relationship is weak and causality is unlikely. The purpose of the present study is to review the strength of association and likelihood of a causal relationship between use of calcitonin and cancer. We reviewed the evidence for this association, including the molecular signaling mechanisms of calcitonin, preclinical data, an "experiment of nature," and the results of a previous meta-analysis which showed a weak association. We performed an additional meta-analysis to incorporate the data from a novel investigational oral formulation of salmon calcitonin. Review of the literature did not identify a cellular signaling mechanism of action which might account for a causal relationship or toxicologic or postmarketing data to support the thesis. Additional clinical results incorporated into previous meta-analyses weakened but did not completely negate the possibility of association. A causal association between calcitonin use and malignancy is unlikely, as there is little biological plausibility. The preponderance of nonclinical and clinical evidence also does not favor a causal relationship.

Context-dependent GluN2B-selective inhibitors of NMDA receptor function are neuroprotective with minimal side effects

Stroke remains a significant problem despite decades of work on neuroprotective strategies. NMDA receptor (NMDAR) antagonists are neuroprotective in preclinical models, but have been clinically unsuccessful, in part due to side effects. Here we describe a prototypical GluN2B-selective antagonist with an IC50 value that is 10-fold more potent at acidic pH 6.9 associated with ischemic tissue compared to pH 7.6, a value close to the pH in healthy brain tissue. This should maximize neuroprotection in ischemic tissue while minimizing on-target side effects associated with NMDAR blockade in noninjured brain regions. We have determined the mechanism underlying pH-dependent inhibition and demonstrate the utility of this approach in vivo. We also identify dicarboxylate dimers as a novel proton sensor in proteins. These results provide insight into the molecular basis of pH-dependent neuroprotective NMDAR block, which could be beneficial in a wide range of neurological insults associated with tissue acidification.

Impact of coexistence of flocs and biofilm on performance of combined nitritation-anammox granular sludge reactors

Nitrogen (N) removal from high-strength wastewater can be accomplished in single-stage combined nitritation-anammox reactors with suspended growth biomass composed of floccular sludge, granular sludge, or of any mix of these 2 different sludge fractions. To date, the influence of floccular biomass on granular sludge reactor performance and stability has not been investigated experimentally or numerically. To address this knowledge gap, two 1D multi-species models were developed in Aquasim to assess the importance of small levels of flocs in putatively granular sludge combined nitritation-anammox reactors for different bulk oxygen concentrations and organics loads. The models included the growth and decay of aerobic ammonium-oxidizing organism (AOO), nitrite-oxidizing organisms (NOO), heterotrophic organisms (OHO), and anammox organisms (AMO) in exclusively granular sludge reactors, and in granular sludge reactors with small levels (∼5% of total biomass) of flocs. While maximum N removal efficiencies were similar for both model structures, floc addition led to a lower optimal dissolved oxygen concentration (DO) as well as a narrower maximum N removal peak, suggesting that small levels of floccular material may decrease process robustness to bulk oxygen changes. For some DO levels, this led to drastic efficiency drops. Furthermore, floc addition also led to substantial segregation in activity and microbial population distribution, with AOO, NOO and OHO concentrated in flocs and AMO concentrated in granules. Increased organic loading (COD:N = 4:3) improved maximum N removal efficiency in both model structures, but yielded substantially different predictions for optimal DO setpoint and process robustness to variations in DO. Taken together, our results indicate that even small levels of floccular biomass in biofilm reactors can have profound implications for reactor performance and optimization and for segregation of linked microbial processes, and suggest that the common practice of neglecting small levels of floccular material in biofilm models and in practice may lead to erroneous predictions.

Antiviral atropisomers: conformational energy surfaces by NMR for host-directed myxovirus blockers

Biologically active organic molecules characterized by a high single bond torsional barrier generate isolable isomers (atropisomers) and offer a unique stereochemical component to the design of selective therapeutic agents. The present work presents a nanomolar active inhibitor of myxoviruses, which most likely acts by blocking one or more cellular host proteins but also, serendipitously, exhibits axial chirality with an energy barrier of ΔG((++)) ≥30 kcal/mol. The latter has been probed by variable temperature NMR and microwave irradiation and by high level DFT transition state analysis and force field calculations. Full conformational profiles of the corresponding (aR,S) and (aS,S) atropisomers at ambient temperature were derived by conformer deconvolution with NAMFIS (NMR Analysis by Molecular Flexibility In Solution) methodology to generate seven and eight individual conformations, each assigned a % population. An accurate evaluation of a key torsion angle at the center of the molecules associated with a (3)JC-S-C-H coupling constant was obtained by mapping the S-C bond rotation with the MPW1PW91/6-31G-d,p DFT method followed by fitting the resulting dihedral angles and J-values to a Karplus expression. Accordingly, we have developed a complete conformational profile of diastereomeric atropisomers consistent with both high and low rotational barriers. We expect this assessment to assist the rationalization of the selectivity of the two (aR,S) and (aS,S) forms against host proteins, while offering insights into their divergent toxicity behavior.

Regulation of GluA1 α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor function by protein kinase C at serine-818 and threonine-840

Three residues within the AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor subunit GluA1 C terminus (Ser818, Ser831, Thr840) can be phosphorylated by Ca(2+)/phospholipid-dependent protein kinase (PKC). Here, we show that PKC phosphorylation of GluA1 Ser818 or Thr840 enhances the weighted mean channel conductance without altering the response time course or agonist potency. These data support the idea that these residues constitute a hyper-regulatory domain for the AMPA receptor. Introduction of phosphomimetic mutations increases conductance only at these three sites within the proximal C terminus, consistent with a structural model with a flexible linker connecting the distal C-terminal domain to the more proximal domain containing a helix bracketed by Ser831 and Thr840. NMR spectra support this model and raise the possibility that phosphorylation can alter the configuration of this domain. Our findings provide insight into the structure and function of the C-terminal domain of GluA1, which controls AMPA receptor function and trafficking during synaptic plasticity in the central nervous system.