Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

BACKGROUND

While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood.

METHODS

Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study.

RESULTS

Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs.

CONCLUSIONS

By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.

The angiopoietin receptor Tie2 is atheroprotective in arterial endothelium

Leukocytes and resident cells in the arterial wall contribute to atherosclerosis, especially at sites of disturbed blood flow. Expression of endothelial Tie1 receptor tyrosine kinase is enhanced at these sites, and attenuation of its expression reduces atherosclerotic burden and decreases inflammation. However, Tie2 tyrosine kinase function in atherosclerosis is unknown. Here we provide genetic evidence from humans and from an atherosclerotic mouse model to show that TIE2 is associated with protection from coronary artery disease. We show that deletion of Tie2, or both Tie2 and Tie1, in the arterial endothelium promotes atherosclerosis by increasing Foxo1 nuclear localization, endothelial adhesion molecule expression and accumulation of immune cells. We also show that Tie2 is expressed in a subset of aortic fibroblasts, and its silencing in these cells increases expression of inflammation-related genes. Our findings indicate that unlike Tie1, the Tie2 receptor functions as the dominant endothelial angiopoietin receptor that protects from atherosclerosis.

Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes

BACKGROUND

Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies have identified over 175 loci associated with CAD. The majority of these loci are in noncoding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we aimed to identify the subset of the CAD loci associated with the regulation of transcription in distinct SMC phenotypes.

METHODS

We measured gene expression in SMCs isolated from the ascending aortas of 151 heart transplant donors of various genetic ancestries in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single-nucleotide polymorphism markers across the genome.

RESULTS

We identified 4910 expression and 4412 splicing quantitative trait loci (sQTLs) representing regions of the genome associated with transcript abundance and splicing. A total of 3660 expression quantitative trait loci (eQTLs) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 eQTLs were SMC-specific and sex-biased, respectively. We made these results available for public query on a user-friendly website. To identify the effector transcript(s) regulated by CAD loci, we used 4 distinct colocalization approaches. We identified 84 eQTL and 164 sQTL that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. One CAD locus colocalized with a sex-specific eQTL (TERF2IP), and another locus colocalized with SMC-specific eQTL (ALKBH8). The most significantly associated CAD locus, 9p21, was an sQTL for the long noncoding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs.

CONCLUSIONS

Collectively, our results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.

The reliability of the angle of deviation measurement from the Photo-Hirschberg tests and Krimsky tests

OBJECTIVE

To compare the angle of deviation measured from Photo-Hirschberg testing and Krimsky testing, with that from an alternate prism cover test (APCT) in strabismus patients.

METHODS

A cross-sectional study was conducted in Songklanagarind Hospital, Thailand. Thirty-three strabismus patients were photographed for analysis by Photo-Hirschberg testing using computer software. The corneal light reflex displacement, converted into prism diopter (PD), was compared to the angle of deviation measured with APCT. Twenty-eight strabismus patients were tested with the Krimsky test. Data were analyzed using Pearson correlation and paired t-tests. The study excluded 4 intermittent exotropia cases, 1 intermittent esotropia case and 2 which cases missing data for krimsky test.

RESULTS

The mean±SD of the deviation angle, measured by APCT with a fixation target at 30 cm and 6 m; were 48.09±16.34PD and 47.82±15.73 PD, respectively. At 1 m, the difference in the angle of deviation measured from APCT and the Photo-Hirschberg test within 10 PD were 58.8% and 63.6%, for ET and XT, respectively. The difference in the angle of deviation measured from APCT and Krimsky tests within 10 PD in ET and XT were 86.7% and 80.0%, respectively. At 4 m, the difference in angle of deviation measured from APCT and Photo-Hirschberg tests within 10 PD in ET and XT were 58.8% and 54.5%, respectively; whereas, the difference in the angle of deviation measured from APCT and Krimsky tests within 10 PD in ET and XT were 80.0% and 70.0%, respectively.

CONCLUSION

The reliability of Krimsky test was better than Photo-Hirschberg test for measuring an angle of deviation.

Evolutionarily conserved exon definition interactions with U11 snRNP mediate alternative splicing regulation on U11-48K and U11/U12-65K genes

Many splicing regulators bind to their own pre-mRNAs to induce alternative splicing that leads to formation of unstable mRNA isoforms. This provides an autoregulatory feedback mechanism that regulates the cellular homeostasis of these factors. We have described such an autoregulatory mechanism for two core protein components, U11-48K and U11/U12-65K, of the U12-dependent spliceosome. This regulatory system uses an atypical splicing enhancer element termed USSE (U11 snRNP-binding splicing enhancer), which contains two U12-type consensus 5' splice sites (5'ss). Evolutionary analysis of the USSE element from a large number of animal and plant species indicate that USSE sequence must be located 25-50 nt downstream from the target 3' splice site (3'ss). Together with functional evidence showing a loss of USSE activity when this distance is reduced and a requirement for RS-domain of U11-35K protein for 3'ss activation, our data suggests that U11 snRNP bound to USSE uses exon definition interactions for regulating alternative splicing. However, unlike standard exon definition where the 5'ss bound by U1 or U11 will be subsequently activated for splicing, the USSE element functions similarly as an exonic splicing enhancer and is involved only in upstream splice site activation but does not function as a splicing donor. Additionally, our evolutionary and functional data suggests that the function of the 5'ss duplication within the USSE elements is to allow binding of two U11/U12 di-snRNPs that stabilize each others' binding through putative mutual interactions.

Crystal Structure of an Engineered LRRTM2 Synaptic Adhesion Molecule and a Model for Neurexin Binding

Synaptic adhesion molecules are key components in development of the brain, and in the formation of neuronal circuits, as they are central in the assembly and maturation of chemical synapses. Several families of neuronal adhesion molecules have been identified such as the neuronal cell adhesion molecules, neurexins and neuroligins, and in particular recently several leucine-rich repeat proteins, e.g., Netrin G-ligands, SLITRKs, and LRRTMs. The LRRTMs form a family of four proteins. They have been implicated in excitatory glutamatergic synapse function and were specifically characterized as ligands for neurexins in excitatory synapse formation and maintenance. In addition, LRRTM3 and LRRTM4 have been found to be ligands for heparan sulfate proteoglycans, including glypican. We report here the crystal structure of a thermostabilized mouse LRRTM2, with a Tm 30 °C higher than that of the wild-type protein. We localized the neurexin binding site to the concave surface based on protein engineering, sequence conservation, and prior information about the interaction of the ligand with neurexins, which allowed us to propose a tentative model for the LRRTM-neurexin interaction complex. We also determined affinities of the thermostabilized LRRTM2 and wild-type LRRTM1 and LRRTM2 for neurexin-β1 with and without Ca(2+). Cell culture studies and binding experiments show that the engineered protein is functional and capable of forming synapselike contacts. The structural and functional data presented here provide the first structure of an LRRTM protein and allow us to propose a model for the molecular mechanism of LRRTM function in the synaptic adhesion.

Mortality and cause of death in abuth, zaria: 1999 - 2005

BACKGROUND

Accurate mortality statistics are needed for policy formulation, implementation and monitoring of health intervention that are aimed at improving the health status of the people. Mortality level is one of the indicators of the quality of life and status of health of a population. However, accurate collection, collation, analysis and interpretation of such data is poorly organised in developing nations, including Nigeria leading to a gap in health policy formulation, implementation and monitoring. Therefore, policies and strategies for disease prevention are based on empirical evidence rather than on data primarily collected to formulate disease specific interventions. Though, hospital data have inherent deficiency in its use to design prevention. However, when accurately generated and adequately managed would provide both qualitative and quantitative information on morbidity and mortality if not for the entire society at least for a segment of the population utilizing it. We implemented a system of death certification to determine causes and pattern of mortality in Ahmadu Bello University Teaching Hospital, Zaria.

METHODS

From May 1999 to November 2005, all case folders of deceased patients were retrieved from the central library of health information management department of the hospital; case folders of deceased patients are required to have in them a completed IFMCCD (International Form of Medical Certification of Cause of Death). All case folders of deceased patients after relevant information were extracted by the staff of health management information department, were passed on to the staff of department of Community Medicine directly involved in this study. The completed cause of death certificates received in the department of Community Medicine (between May 1999 and November 2005), were examined. Coding rules were employed to select the appropriate code for those certificates that were incorrectly completed. The underlying cause of death as identified from the correctly completed IFMCCDS is coded according to ICD-10.

RESULTS

For the period under study, there were 4019 deaths: 2212 males and 1807 females. Total of 2914 (72.5%) deaths were certified, using the IFMCCD of which 1641 of them were males and 1273 females and formed the basis of this analysis. Coverage rates ranges from 56.2% in 2001 to 85% in 1999. The proportion of garbage codes ranges from 0% to 2.4% while the three leading causes of death are HIV infection, road traffic accident (RTA), and cardiovascular diseases among the ten. The time-trend of the leading causes of death show RTA maintaining steady upward climb while malaria, septicemia, PEM, sepsis in the neonatal period shows unsteady fluctuation.

CONCLUSION

This study assessed the pattern of mortality and causes of death in ABU Teaching Hospital, Zaria; it also provided information on leading causes of death.

Evaluation of the diethylcarbamazine provocative test in the diagnosis of Wuchereria bancrofti infections in the Nigerian savanna and the effects on Dipetalonema perstans

Large scale filariasis surveys in rural areas for microfilaraemia, especially of periodic types such as Wuchereria bancrofti are known to cause considerable administrative, technical and social problems. The present investigation was carried out in the population of two villages in the Malumfashi district of the Northern Nigerian savanna. From the survey results, the sensitivity and specificity of two techniques-day-time diethylcarbamazine (DEC) provocative test by blood smear and concentration, and night-blood examination by smear and concentration especially for W. bancrofti-were assessed. Day-time DEC provocative test proved to be efficient in terms of sensitivity and specificity, compared with the night-blood method, for W. bancrofti detection but less so for Dipetalonema perstans, the other blood microfilaria found in this population during these studies. A regression line between night-blood survey results for W. bancrofti and the results from day-time DEC provocative test was calculated. With the help of this regression line it is possible to estimate W. bancrofti microfilarial prevalence for night surveys, using the DEC provocative test results of day-time surveys. This can be done with minimal, but known, loss of accuracy and incurs fewer administrative, technical and social difficulties.

Effectiveness of oral killed typhoid vaccine

A controlled field trial of oral killed typhoid vaccine was carried out in Delhi, India in 1968-69. Altogether, 13 374 children below the age of 17 years were included in the study. Two comparable groups of children were given either placebo or vaccine. Each tablet of vaccine contained 100x10(9) killed Salmonella typhi, and 3 tablets of vaccine or placebo were administered to each child. The vaccinated subjects were followed up from 10 June 1968 to 31 August 1969. The effectiveness of the vaccine was measured by comparing the incidence of typhoid fever (based only on bacteriologically positive cases) in the two groups. It was found that the difference in incidence of the disease in the two groups was not statistically significant. The oral killed typhoid vaccine in the dosage schedule used in the present trial was found not to be effective against the disease.