Fetal biometry and amniotic fluid volume assessment end-to-end automation using Deep Learning

Fetal biometry and amniotic fluid volume assessments are two essential yet repetitive tasks in fetal ultrasound screening scans, aiding in the detection of potentially life-threatening conditions. However, these assessment methods can occasionally yield unreliable results. Advances in deep learning have opened up new avenues for automated measurements in fetal ultrasound, demonstrating human-level performance in various fetal ultrasound tasks. Nevertheless, the majority of these studies are retrospective in silico studies, with a limited number including African patients in their datasets. In this study we developed and prospectively assessed the performance of deep learning models for end-to-end automation of fetal biometry and amniotic fluid volume measurements. These models were trained using a newly constructed database of 172,293 de-identified Moroccan fetal ultrasound images, supplemented with publicly available datasets. the models were then tested on prospectively acquired video clips from 172 pregnant people forming a consecutive series gathered at four healthcare centers in Morocco. Our results demonstrate that the 95% limits of agreement between the models and practitioners for the studied measurements were narrower than the reported intra- and inter-observer variability among expert human sonographers for all the parameters under study. This means that these models could be deployed in clinical conditions, to alleviate time-consuming, repetitive tasks, and make fetal ultrasound more accessible in limited-resource environments.

Blockage of lamin-A/C loss diminishes the pro-inflammatory macrophage response

Mutations and defects in nuclear lamins can cause major pathologies, including inflammation and inflammatory diseases. Yet, the underlying molecular mechanisms are not known. We now report that the pro-inflammatory activation of macrophages, as induced by LPS or pathogenic E. coli, reduces Lamin-A/C levels thereby augmenting pro-inflammatory gene expression and cytokine secretion. We show that the activation of bone-marrow-derived macrophages (BMDMs) causes the phosphorylation and degradation of Lamin-A/C, as mediated by CDK1 and Caspase-6, respectively, necessary for upregulating IFN-β expression. Enhanced IFN-β expression subsequently increases pro-inflammatory gene expression via the IFN-β-STAT axis. Pro-inflammatory gene expression was also amplified in the complete absence of Lamin-A/C. Alternatively, pharmacological inhibition of either Lamin-A/C phosphorylation or degradation significantly downregulated pro-inflammatory gene expression, as did the targeting of IFN-β-STAT pathway members, i.e. phospho-STAT1 and phospho-STAT3. As Lamin-A/C is a previously unappreciated regulator of the pro-inflammatory macrophage response, our findings suggest novel opportunities to treat inflammatory diseases.

Abstract 396: CHROMR Coordinates Interferon Signaling And Lipid Metabolism In Viral Infection

COVID-19, caused by SARS-CoV-2 infection, is associated with atherosclerotic cardiovascular complications like acute coronary syndrome, myocardial infarction, and stroke, but the underlying mechanisms are poorly understood. Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression in the immune response. RNA-seq of whole blood from hospitalized patients with COVID-19, influenza A virus and matched controls identified 190 lncRNAs deregulated in both viral infections. Among the top mutually upregulated lncRNAs, we noted CHROMR (alias CHROME ) , a primate-specific lncRNA previously identified as a competing endogenous RNA that regulates cholesterol efflux and fatty acid oxidation via microRNA sequestration. Here, we report a complementary role for CHROMR in coordinating the interferon (IFN) signaling response to respiratory viruses. CHROMR expression is induced in macrophages in response to SARS-CoV-2 and influenza A infection and accumulates in the nucleus where it binds the transcriptional co-repressor IRF2BP2, a negative regulator of IFN-stimulated gene (ISG) expression. CHROMR is essential for mounting an anti-viral response, as its depletion in macrophages reduces histone acetylation at ISGs, activation of IRF signaling, and ISG expression. These findings suggest that CHROMR sequesters the nuclear IRF-2/IRF2BP2 repressor complex releasing its inhibitory effect on transcription of ISGs. Consistent with this, CHROMR expression is required to restrict influenza virus replication in macrophages. Notably, many viruses rewire host lipid synthesis and metabolism to facilitate replication, and thus, increased CHROMR expression in virus infected cells would both mitigate cellular lipid accumulation and increase ISG transcription to mount an anti-viral immune response. Collectively, our findings underscore the merit of investigating lncRNAs to decipher novel regulatory mechanisms that govern lipid metabolism and inflammation in humans.

The Set7 Lysine Methyltransferase Regulates Plasticity in Oxidative Phosphorylation Necessary for Trained Immunity Induced by β-Glucan

Trained immunity confers a sustained augmented response of innate immune cells to a secondary challenge, via a process dependent on metabolic and transcriptional reprogramming. Because of its previous associations with metabolic and transcriptional memory, as well as the importance of H3 histone lysine 4 monomethylation (H3K4me1) to innate immune memory, we hypothesize that the Set7 methyltransferase has an important role in trained immunity induced by β-glucan. Using pharmacological studies of human primary monocytes, we identify trained immunity-specific immunometabolic pathways regulated by Set7, including a previously unreported H3K4me1-dependent plasticity in the induction of oxidative phosphorylation. Recapitulation of β-glucan training in vivo additionally identifies Set7-dependent changes in gene expression previously associated with the modulation of myelopoiesis progenitors in trained immunity. By revealing Set7 as a key regulator of trained immunity, these findings provide mechanistic insight into sustained metabolic changes and underscore the importance of characterizing regulatory circuits of innate immune memory.

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Set7 regulates enhanced cytokine production in trained immunity in vitro

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Set7 knockout mice are unable to mount trained immunity against endotoxin challenge

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Set7 modulates cellular respiration in β-glucan-trained macrophages

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Set7-dependent histone methylation regulates MDH2 and SDHB in trained cells

Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes

Mycobacterium tuberculosis possesses a large number of genes of unknown or predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular chromosomal localizations in the related non-pathogen, M. smegmatis. Applying automated imaging and analysis to 263 essential gene knockdown mutants in an arrayed library, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to inform investigations of gene function. Exploiting this observation, we infer the existence of a mycobacterial restriction-modification system, and identify filamentation as a defining mycobacterial response to histidine starvation. Our results support the application of large-scale image-based analyses for mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.

FRI0014 A PUTATIVE ROLE OF IGF-1R ON THE PATHOGENESIS OF GOUT THROUGH BINDING TO TRANSCRIPTION FACTORS

Background:

Recent studies showed that SNPs on IGF-1/IGF-1R were highly associated with hyperuricemia and gout [1,2]. It was shown that the IGF-1/IGF-1R signaling pathway played a role in regulating the serum urate level. By modulating the uric acid transporters, IGF-1/IGF-1R influenced the resorption and secretion of uric acid. However, we demonstrated that the increased activation of IGF1R could activate the mTOR pathway, leading to a higher inflammatory response upon pathogen stimulation [3]. This finding indicates that IGF-1/IGF1-R has a role in inflammation, which could results in gout. The IGF-1/IGF-1R pathway may have an overall influence on both urate transporters and inflammatory pathways. it was shown that IGF-1R was not only expressed on the cell surface, but could also internalize into the nucleus and recruit RNA polymerase, regulating the expression of other transcription factors[4]. These transcription factors have been shown to regulate inflammation and have been predicted to bind promoter regions of urate transporters [5]

Objectives:

To unveil how the IGF-1/IGF1-R associates with hyperuricemia and gout by studying the IGF-1R SNP rs6598541.

Methods:

To assess the influence of the SNP to IGF1-R, the protein expression of IGF-1R on the cell surface was identified by flow cytometry in different genotypes. Additionally, we measured the in vitro immune response of PBMCs with different genotypes upon exposure to MSU and/or LPS. To estimate the overall influence of the SNP on the immune response, we analyzed the SNP’s function on transcription factors.

Results:

We observed an enhanced inflammatory response in the homozygous genotype with the risk alleles upon LPS and/or MSU stimulation, indicative of a higher risk for gout. However, the IGF-1R surface expression level was comparable between different genotypes. Furthermore, in epigenetic analysis, we found that rs6598541 located in an enhancer region, which is bound by c-FOS, c-JUN and other transcription factors. In recent years, c-FOS and c-JUN have been shown to regulate inflammatory responses.

Conclusion:

The risk allele of rs6598541 is associated with a higher inflammatory response, which might be the key factor for gout. Because of the location of the SNP, it might explain the function of IGF-1R in gout, and the pathogenesis might be modulated through transcription factors. According to the recent study, intracellular IGF-1R could act as a transcription factor regulating other transcription factors expression, like c-JUN. Additionally, c-JUN has been shown to regulate inflammatory responses. It is tempting to speculate that IGF-1R regulates transcription factors expression and leads to an overall immune responses, which influence the risk of gout.

References:

[1]Kottgen, A., et al.,Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.Nat Genet, 2013.45(2): p. 145-54.

[2]Mannino, G.C., et al.,The polymorphism rs35767 at IGF1 locus is associated with serum urate levels.Sci Rep, 2018.8(1): p. 12255.

[3]Bekkering, S., et al.,Metabolic Induction of Trained Immunity through the Mevalonate Pathway.Cell, 2018.172(1-2): p. 135-146.e9.

[4]Aleksic, T., et al.,Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage.Cancer Res, 2018.78(13): p. 3497-3509.

[5]Granet, C., W. Maslinski, and P. Miossec,Increased AP-1 and NF-kappaB activation and recruitment with the combination of the proinflammatory cytokines IL-1beta, tumor necrosis factor alpha and IL-17 in rheumatoid synoviocytes.Arthritis Res Ther, 2004.6(3): p. R190-8.

Disclosure of Interests:

Ruiqi Liu: None declared, Orsi Gaal: None declared, Viola Klück: None declared, Tania Crisan: None declared, Stephanie Fanucchi: None declared, Musa Mhlanga: None declared, Leo Joosten Consultant of: SAB member of Olatec Therapeutics LLC

Evaluating capacity at three government referral hospital emergency units in the kingdom of Eswatini using the WHO Hospital Emergency Unit Assessment Tool

BACKGROUND

The Kingdom of Eswatini, a lower-middle income nation of 1.45 million in southern Africa, has recently identified emergency care as a key strategy to respond to the national disease burden. We aimed to evaluate the current capacity of hospital emergency care areas using the WHO Hospital Emergency Unit Assessment Tool (HEAT) at government referral hospitals in Eswatini.

METHODS

We conducted a cross-sectional study of three government referral hospital emergency care areas using HEAT in May 2018. This standardised tool assists healthcare facilities to assess the emergency care delivery capacity in facilities and support in identifying gaps and targeting interventions to strengthen care delivery within emergency care areas. Senior-level emergency care area employees, including senior medical officers and nurse matrons, were interviewed using the HEAT.

RESULTS

All sites provided some level of emergency care 24 h a day, 7 days a week, though most had multiple entry points for emergency care. Only one facility had a dedicated area for receiving emergencies and a dedicated resuscitation area; two had triage areas. Facilities had limited capacity to perform signal functions (life-saving procedures that require both skills and resources). Commonly reported barriers included training deficits and lack of access to supplies, medications, and equipment. Sites also lacked formal clinical management and process protocols (such as triage and clinical protocols).

CONCLUSIONS

The HEAT highlighted strengths and weaknesses of emergency care delivery within hospitals in Eswatini and identified specific causes of these system and service gaps. In order to improve emergency care outcomes, multiple interventions are needed, including training opportunities, improvement in supply chains, and implementation of clinical and process protocols for emergency care areas. We hope that these findings will allow hospital administrators and planners to develop effective change management plans.

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection

Background

Tuberculosis is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M.tb). M.tb subverts host immune responses to build a favourable niche and survive inside of host macrophages. Macrophages can control or eliminate the infection, if acquire appropriate functional phenotypes. Transcriptional regulation is a key process that governs the activation and maintenance of these phenotypes. Among the factors orchestrating transcriptional regulation during M.tb infection, transcriptional enhancers still remain unexplored.

Results

We analysed transcribed enhancers in M.tb-infected mouse bone marrow-derived macrophages. We established a link between known M.tb-responsive transcription factors and transcriptional activation of enhancers and their target genes. Our data suggest that enhancers might drive macrophage response via transcriptional activation of key immune genes, such as Tnf, Tnfrsf1b, Irg1, Hilpda, Ccl3, and Ccl4. We report enhancers acquiring transcription de novo upon infection. Finally, we link highly transcriptionally induced enhancers to activation of genes with previously unappreciated roles in M.tb infection, such as Fbxl3, Tapt1, Edn1, and Hivep1.

Conclusions

Our findings suggest the importance of macrophage host transcriptional enhancers during M.tb infection. Our study extends current knowledge of the regulation of macrophage responses to M.tb infection and provides a basis for future functional studies on enhancer-gene interactions in this process.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5450-6) contains supplementary material, which is available to authorized users.

Work-related musculoskeletal disorders among registered general nurses: a case of a large central hospital in Harare, Zimbabwe

Objective

Worldwide, work-related musculoskeletal disorders (WMSDs) are a common cause of morbidity affecting occupational individuals such as health-care professionals. However, nothing is known about WMSDs in hospital nurses in Zimbabwe. This study was conducted to provide cross-sectional evidence of the 12-month prevalence, consequences and factors associated with WMSDs among 208 nurses at Parirenyatwa Group of Hospitals (PGH).

Results

The response rate for the study was 55.7%. The median age for the participants was 32.0 years (interquartile range = 29–36 years). The lifetime prevalence of WMSDs in nurses was 95.7% (n = 112). The first episodes were experienced in the first 5 years of working (n = 59, 52.7%). However, 82.1% (n = 96) nurses experienced WMSDs in the last 12 months. Low back pain was the most common WMSDs reported (n = 55, 67.9%). WMSDs were significantly associated with qualification attained, postgraduate ergonomic training and working experience. Overall, 87.5% (n = 84) nurses experienced at least one of the consequences of WMSDs. Cognisant of the limitations of the study, the present study found that WMSDs are a common occurrence among nurses at PGH. This creates a need for prompt hospital education programs aimed at raising awareness among nurses on the existence of WMSDs and the consequences at PGH.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3412-8) contains supplementary material, which is available to authorized users.

Three parallel information systems for malaria elimination in Swaziland, 2010-2015: are the numbers the same?

Background: To be able to eliminate malaria, accurate, timely reporting and tracking of all confirmed malaria cases is crucial. Swaziland, a country in the process of eliminating malaria, has three parallel health information systems. Design: This was a cross-sectional study using country-wide programme data from 2010 to 2015. Methods: The Malaria Surveillance Database System (MSDS) is a comprehensive malaria database, the Immediate Disease Notification System (IDNS) is meant to provide early warning and trigger case investigations to prevent onward malaria transmission and potential epidemics, and the Health Management Information Systems (HMIS) reports on all morbidity at health facility level. Discrepancies were stratified by health facility level and type. Results: Consistent over-reporting of 9-85% was noticed in the HMIS, principally at the primary health care level (clinic and/or health centre). In the IDNS, the discrepancy went from under-reporting (12%) to over-reporting (32%); this was also seen at the primary care level. At the hospital level, there was under-reporting in both the HMIS and IDNS. Conclusions: There are considerable discrepancies in the numbers of confirmed malaria cases in the HMIS and IDNS in Swaziland. This may misrepresent the malaria burden and delay case investigation, predisposing the population to potential epidemics. There is an urgent need to improve data integrity in order to guide and evaluate efforts toward elimination.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

Nanoscopic Localization of Surface-Exposed Antigens of Borrelia burgdorferi

Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, is transmitted to humans through the bite of infected Ixodes spp. ticks. Successful infection of vertebrate hosts necessitates sophisticated means of the pathogen to escape the vertebrates' immune system. One strategy employed by Lyme disease spirochetes to evade adaptive immunity involves a highly coordinated regulation of the expression of outer surface proteins that is vital for infection, dissemination, and persistence. Here we characterized the expression pattern of bacterial surface antigens using different microscopy techniques, from fluorescent wide field to super-resolution and immunogold-scanning electron microscopy. A fluorescent strain of B. burgdorferi spirochetes was labeled with monoclonal antibodies directed against various bacterial surface antigens. Our results indicate that OspA is more evenly distributed over the surface than OspB and OspC that were present as punctate areas.

TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures

Nuclear factor κB (NF-κB) essential modulator (NEMO), a regulatory component of the IκB kinase (IKK) complex, controls NF-κB activation through its interaction with ubiquitin chains. We show here that stimulation with interleukin-1 (IL-1) and TNF induces a rapid and transient recruitment of NEMO into punctate structures that are anchored at the cell periphery. These structures are enriched in activated IKK kinases and ubiquitinated NEMO molecules, which suggests that they serve as organizing centers for the activation of NF-κB. These NEMO-containing structures colocalize with activated TNF receptors but not with activated IL-1 receptors. We investigated the involvement of nondegradative ubiquitination in the formation of these structures, using cells deficient in K63 ubiquitin chains or linear ubiquitin chain assembly complex (LUBAC)-mediated linear ubiquitination. Our results indicate that, unlike TNF, IL-1 requires K63-linked and linear ubiquitin chains to recruit NEMO into higher-order complexes. Thus, different mechanisms are involved in the recruitment of NEMO into supramolecular complexes, which appear to be essential for NF-κB activation.

Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens

Influenza virus encodes only 11 viral proteins but replicates in a broad range of avian and mammalian species by exploiting host cell functions. Genome-wide RNA interference (RNAi) has proven to be a powerful tool for identifying the host molecules that participate in each step of virus replication. Meta-analysis of findings from genome-wide RNAi screens has shown influenza virus to be dependent on functional nodes in host cell pathways, requiring a wide variety of molecules and cellular proteins for replication. Because rapid evolution of the influenza A viruses persistently complicates the effectiveness of vaccines and therapeutics, a further understanding of the complex host cell pathways coopted by influenza virus for replication may provide new targets and strategies for antiviral therapy. RNAi genome screening technologies together with bioinformatics can provide the ability to rapidly identify specific host factors involved in resistance and susceptibility to influenza virus, allowing for novel disease intervention strategies.

Transcriptome dysregulation by anthrax lethal toxin plays a key role in induction of human endothelial cell cytotoxicity

We have investigated how Bacillus anthracis lethal toxin (LT) triggers caspase-3 activation and the formation of thick actin cables in human endothelial cells. By DNA array analysis we show that LT has a major impact on the cell transcriptome and we identify key host genes involved in LT cytotoxic effects. Indeed, upregulation of TRAIL and downregulation of XIAP both participate in LT-induced caspase-3 activation. LT induces a downregulation of the immediate early gene and master regulator of transcription egr1. Importantly, its re-expression in LT-intoxicated cells blocks caspase-3 activation. In parallel, we found that the formation of actin cables induced by LT occurs in the absence of direct activation of RhoA/ROCK signalling. We show that knock-down of cortactin and rhophilin-2 under conditions of calponin-1 expression defines the minimal set of genes regulated by LT for actin cable formation. Together our data establish that the modulation of the cell transcriptome by LT plays a key role in triggering human endothelial cell toxicity.