Network Preservation Analysis Reveals Dysregulated Metabolic Pathways in Human Vascular Smooth Muscle Cell Phenotypic Switching

BACKGROUND

Vascular smooth muscle cells are key players involved in atherosclerosis, the underlying cause of coronary artery disease. They can play either beneficial or detrimental roles in lesion pathogenesis, depending on the nature of their phenotypic changes. An in-depth characterization of their gene regulatory networks can help better understand how their dysfunction may impact disease progression.

METHODS

We conducted a gene expression network preservation analysis in aortic smooth muscle cells isolated from 151 multiethnic heart transplant donors cultured under quiescent or proliferative conditions.

RESULTS

We identified 86 groups of coexpressed genes (modules) across the 2 conditions and focused on the 18 modules that are least preserved between the phenotypic conditions. Three of these modules were significantly enriched for genes belonging to proliferation, migration, cell adhesion, and cell differentiation pathways, characteristic of phenotypically modulated proliferative vascular smooth muscle cells. The majority of the modules, however, were enriched for metabolic pathways consisting of both nitrogen-related and glycolysis-related processes. Therefore, we explored correlations between nitrogen metabolism-related genes and coronary artery disease-associated genes and found significant correlations, suggesting the involvement of the nitrogen metabolism pathway in coronary artery disease pathogenesis. We also created gene regulatory networks enriched for genes in glycolysis and predicted key regulatory genes driving glycolysis dysregulation.

CONCLUSIONS

Our work suggests that dysregulation of vascular smooth muscle cell metabolism participates in phenotypic transitioning, which may contribute to disease progression, and suggests that AMT (aminomethyltransferase) and MPI (mannose phosphate isomerase) may play an important role in regulating nitrogen and glycolysis-related metabolism in smooth muscle cells.

FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells

BACKGROUND

Genome-wide association studies have identified hundreds of loci associated with common vascular diseases, such as coronary artery disease, myocardial infarction, and hypertension. However, the lack of mechanistic insights for many GWAS loci limits their translation into the clinic. Among these loci with unknown functions is UFL1-four-and-a-half LIM (LIN-11, Isl-1, MEC-3) domain 5 (FHL5; chr6q16.1), which reached genome-wide significance in a recent coronary artery disease/ myocardial infarction GWAS meta-analysis. UFL1-FHL5 is also associated with several vascular diseases, consistent with the widespread pleiotropy observed for GWAS loci.

METHODS

We apply a multimodal approach leveraging statistical fine-mapping, epigenomic profiling, and ex vivo analysis of human coronary artery tissues to implicate FHL5 as the top candidate causal gene. We unravel the molecular mechanisms of the cross-phenotype genetic associations through in vitro functional analyses and epigenomic profiling experiments in coronary artery smooth muscle cells.

RESULTS

We prioritized FHL5 as the top candidate causal gene at the UFL1-FHL5 locus through expression quantitative trait locus colocalization methods. FHL5 gene expression was enriched in the smooth muscle cells and pericyte population in human artery tissues with coexpression network analyses supporting a functional role in regulating smooth muscle cell contraction. Unexpectedly, under procalcifying conditions, FHL5 overexpression promoted vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites and inferring FHL5 target gene function using artery tissue gene regulatory network analyses, we highlight regulatory interactions between FHL5 and downstream coronary artery disease/myocardial infarction loci, such as FOXL1 and FN1 that have roles in vascular remodeling.

CONCLUSIONS

Taken together, these studies provide mechanistic insights into the pleiotropic genetic associations of UFL1-FHL5. We show that FHL5 mediates vascular disease risk through transcriptional regulation of downstream vascular remodeling gene programs. These transacting mechanisms may explain a portion of the heritable risk for complex vascular diseases.

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.

Differentiation of Species and Populations of Aphelenchoides and of Ditylenchus angustus Using a Fragment of Ribosomal DNA

The polymerase chain reaction (PCR) was used to amplify a fragment of the ribosomal DNA (rDNA) from species and undescribed populations of Aphelenchoides and Ditylenchus angustus. The PCR primers used were based on conserved sequences in the 18S and 26S ribosomal RNA genes of Caenorhabditis elegans. In C. elegans, these primers amplify a 1,292 base pair (bp) fragment, which consists of the two internal transcribed spacers and the entire 5.8S gene. Amplification products from crude DNA preparations of 12 species and populations of Aphelenchoides and from D. angustus ranged in size from approximately 860-1,100bp. Southern blots probed with a cloned ribosomal repeat from C. elegans confirmed the identity of these amplified bands as ribosomal fragments. In addition to the differing sizes of the amplified rDNA fragments, the relative intensity of hybridization with the C. elegans probe indicated varying degrees of sequence divergence between species and populations. In some cases, amplified rDNA from the fungal host was evident. Storage of A. composticola at - 45 C for 2 years did not affect the ability to obtain appropriate amplified products from crude DNA preparations. Amplified rDNA fragments were cut with six restriction enzymes, and the restriction fragments produced revealed useful diagnostic differences between species and some undescribed populations. These results were consistent with previous studies based on morphology and isoenzymes. Three undescribed populations of Aphelenchoides were found to be different from all the species examined and from each other.

Analysis of responses of Leidynema appendiculata to acetylcholine using electrophysiological techniques

The electrophysiological responses of adult females of the insect-parasitic nematode Leidynema appendiculata, to 100 mM, 10 mM, and 1 mM acetylcholine were concentration dependent, with stimulation by 100 mM acetylcholine giving the largest increase in spike activity. By contrast, the delay in response was not concentration dependent. No increase in activity was obtained on stimulation with either 0.1 mM acetylcholine or phosphate-buffered saline. The lack of response to 0.1 mM acetylcholine was confirmed by sequential exposure of L. appendiculata to 0.1 mM acetylcholine and subsequently to 10 mM acetylcholine.

Analysis of the sensory responses of parasitic nematodes using electrophysiology

Use of the electrophysiological technique to examine the sensory perception of live, intact nematodes has provided detailed analysis of responses to known concentrations of test chemicals. The use of larger nematodes, such as the animal-parasite Syngamus trachea, enabled direct extracellular recordings from individual sensilla; with smaller nematodes, the recording electrode was inserted close to the cephalic region. Extracellular recordings from the cephalic region of second-stage juveniles and males of the potato cyst nematodes, Globodera rostochiensis and Globodera pallida, were obtained after exposure to a variety of semiochemicals, including sex pheromones and certain putative phagostimulatory compounds. The responses of adult females of the animal-parasitic nematode, Brugia pahangi, to some possible host cues, and the inhibition by ivermectin of the response to a known allelochemical were investigated. Exposure to acetylcholine was used to compare the concentration-dependent responses of second-stage juveniles of G. rostochiensis and adult females of B. pahangi and the insect-parasitic nematode Leidynema appendiculata. Use of a perfusion system enabled sequential exposure of individual nematodes to different test chemicals or to different concentrations of the same chemical. Incubating second-stage juveniles of G. rostochiensis for 24 h in a mAb showing specificity to amphidial secretions resulted in blocking of the normal response to host root diffusates. The potential of the electrophysiology technique for analysing perturbation of sensory perception is discussed.

Desiccation survival of parasitic nematodes

The ability of certain species of parasitic nematodes to survive desiccation for considerable periods is a fascinating example of adaptation to the demands of fluctuating environments that occasionally can become extreme and life threatening. Behavioural and morphological adaptations associated with desiccation survival serve primarily to reduce the rate of drying, either to prolong the time taken for the nematode's water content to reach lethal low levels or, in true anhydrobiotes, to enable the structural and biochemical changes required for long-term survival to take place. Examples of these adaptations are reviewed, together with information on the factors involved in rehydration that ensure successful exit from the dormant state. Information on desiccation survival is central to effective management and control options for parasitic nematodes. It is also required to assess the feasibility of enhancing the longevity of commercial formulations of entomopathogenic nematodes, both before and after application; current research and future prospects for enhancing survival of these bio-insecticides are discussed.

Electrophysiological analysis of responses of adult females of Brugia pahangi to some chemicals

Electrophysiological techniques were used to obtain recordings of extracellular electrical activity from the anterior end of live adult females of Brugia pahangi. Stimulation with 100 mM, 10 mM and 1 mM acetylcholine resulted in an increase in spike activity which was concentration dependent, whereas stimulation with phosphate-buffered saline and 0.1 mM acetylcholine gave no increase in activity. The delay in response was not concentration dependent. The action of possible host cues was investigated. Stimulation with heat-inactivated foetal calf serum (IFCS) and 10 mM glutathione gave an increase in spike activity but exposure to 5 mg/dl haemoglobin elicited no response. The response to IFCS was found to be suppressed completely by pre-incubation for 30 min in ivermectin.

Changes in the lipid content and fatty acid composition of 2nd-stage juveniles of Globodera rostochiensis after rehydration, exposure to the hatching stimulus and hatch

The total lipid content of the dry weight of whole cysts and 2nd-stage juveniles (J2) of Globodera rostochiensis was 17.1% in dry cysts, 20.9% in cysts soaked in distilled water (DW), 20.3% in cysts that had been in potato root diffusate (PRD) for 7 days, 7.3% in cysts that had been in PRD for 28 days and 29.2% for hatched J2. The fatty acid composition of the total lipid did not differ between dry cysts, cysts in DW and cysts in PRD for 7 days. However, major differences in the fatty acid composition of all lipid classes were found between rehydrated cysts in PRD and freshly hatched J2. After hatching, the degree of saturation and the percentage of monounsaturated fatty acids decreased and the percentage of polyunsaturated fatty acids increased considerably, especially in the free fatty acid fraction, where C20:1 showed an 8-fold decrease and C20:4 a 33-fold increase. There was a difference in the fatty acid composition of cysts in PRD for 7 days and cysts in PRD for 28 days (after most of the J2 had hatched); with increased time in PRD the percentage of polyunsaturated fatty acids increased and the percentage of monounsaturated fatty acids decreased in all lipid classes. Differences in the fatty acid profiles between cysts in PRD for 28 days and hatched J2 were found mainly in the free fatty acid and the non-acidic phospholipid fractions. The free fatty acid fraction of the cysts was dominated by monounsaturated fatty acids (52%), whereas the same fraction of hatched J2 contained large amounts of polyunsaturated fatty acids (60%). These polyunsaturated fatty acids, especially C20:4, might play an important part in nematode-plant interactions during infection.

Electrophysiological analysis of the response of males of the potato cyst nematode, Globodera rostochiensis, to fractions of their homospecific sex pheromone

Electrophysiological techniques and behavioural assays were used to determine the response of males of Globodera rostochiensis to 4 fractions of the homospecific sex pheromone from virgin females, separated using reverse-phase high-pressure liquid chromatography. Sex pheromone activity was confined to 2 of the fractions. The sex pheromone of G. rostochiensis appears to be composed of several weakly basic, polar compounds.

Desiccation survival of populations of the entomopathogenic nematodes Steinernema feltiae and Heterorhabditis megidis from Greece and the UK

The desiccation survival and ability to control water loss during drying of individual infective juveniles (IJs) of populations of Steinernema feltiae and Heterorhabditis megidis from Greece and the UK were examined at different relative humidities. Survival at all relative humidities was for minutes only and there was no evidence of enhanced survival of the populations of either species from Greece compared with those from the UK. The survival of individuals of both populations of H. megidis was superior to that of S. feltiae and the rate of drying of H. megidis was significantly slower. The sheath surrounding the IJs of H. megidis appears to be involved in slowing the rate of water loss of the enclosed nematodes.

Desiccation survival and water contents of entomopathogenic nematodes, Steinernema spp. (Rhabditida:Steinernematidae)

The survival of exsheathed infective juveniles (IJs) of 4 Steinernema species, S. glaseri (NC), S. feltiae (UK76), S. carpocapsae (All) and S. riobravis (Biosys355), was assessed following fast and slow drying on glass slides and 1% (w/v) agarose, respectively. Freshly harvested and aged (75-day-old) IJs were desiccated on glass slides after removal of superficial water, at 0, 20, 40, 60 and 80% relative humidity (r.h.). Survival was assessed after rehydration with water, and movement was used as the criterion for survival. Evidence for an intrinsic mechanism to control water loss and survive desiccation was found in freshly harvested S. carpocapsae IJs. At all r.h.s tested, S. carpocapsae had the greatest survival and the slowest rate of water loss. For example, at 80% r.h. the survival time for 50% (S50) of S. carpocapsae IJs was ca. 45 min compared with 5-20 min for the other species. Survival of aged IJs was markedly reduced in the case of S. carpocapsae and S. riobravis, and to a lesser extent in S. feltiae and S. glaseri. The 2nd stage juvenile cuticle (sheath) was not important in aiding desiccation survival of S. carpocapsae and S. glaseri. Drying IJs slowly on 1% agarose at 80% r.h. greatly improved the survival of all 4 species, particularly S. glaseri and S. feltiae. The work is discussed in relation to possible mechanisms for survival of IJs during fast and slow drying.

Chemoreception in plant parasitic nematodes

The role and functioning of the anterior chemosensory organs of plant parasitic nematodes is examined, with particular emphasis on the amphids. The morphology of the amphids is discussed primarily in the context of the changes in the ultrastructure associated with different life stages. The involvement of amphidial secretions in chemoreception and the behavioral and electrophysiological analyses of nematode responses to semiochemicals are discussed with special reference to research on sex pheromones. These research techniques, combined with the use of lectins and antibodies, provide information on nematode sensilla that may lead to novel control strategies for economically important plant parasitic nematodes based on perturbing nematode sensory perception to prevent host or mate location.

Biochemical analyses on single amphidial glands, excretory-secretory gland cells, pharyngeal glands and their secretions from the avian nematode Syngamus trachea

The gape nematode, Syngamus trachea, has been used as a model to study nematode secretions. Individual and intact pairs of amphidial glands, pharyngeal glands and pairs of excretory-secretory gland cells have been dissected and their secretory products analysed. The protein profiles of each gland and the total nematode secretions were analysed on 12.5% homogeneous SDS-PAGE minigels. The protein analyses revealed that the structural protein profile of each gland is different. The amphidial gland secretes two major proteins of 36.0 and 41.5 kDa, the excretory-secretory gland cell secretes a protein of 28.2 kDa and a protein of 14.3 kDa, and the pharyngeal gland secretes proteins of 41.5 and 14.6 kDa. Analysis of the total nematode secretions revealed all of the above major secretory proteins and an additional protein of 49.3 kDa. Syngamus trachea secretes acetylcholinesterases and its secretions contain multiple proteases.

Investigation of the chemosensory function of amphids of Syngamus trachea using electrophysiological techniques

Syngamus trachea, the gape nematode, has been used as a model to study the chemosensory function of amphids. Extracellular electrophysiological recordings were performed directly on amphids. The amphids were stimulated by blood serum from a host bird and by D-tryptophan. The spike frequency produced by the amphid increased significantly after the application of the serum and the application of D-tryptophan. Two types of amphidial neurones responded to the presence of the stimuli. These extracellular recordings have verified the chemosensory function of the amphids.

The Immunofluorescent Localization of Subventral Pharyngeal Gland Epitopes of Preparasitic Juveniles of Heterodera glycines Using Laser Scanning Confocal Microscopy

Laser scanning confocal microscopy (LSCM) was used to localize the reactivity of a monoclonal antibody (Sv2) that binds to the subventral pharyngeal glands of preparasitic juveniles of Heterodera glycines. The greater resolution, magnification, and image analysis of LSCM compared with conventional epifluorescent microscopy enabled Sv2 binding to be localized much more precisely to the periphery of the secretory granules. A linear increase of about 55% in fluorescent intensity was found over a 23-mum length of subventral pharyngeal gland just distal to the terminal ampullae. LSCM is a rapid and effective technique for precise immunolocalization of epitopes.

Dormancy and hatching of nematode eggs

The sequence of events during the hatching process of some parasitic nematodes has been the subject of recent detailed study. Certain factors, such as the trehalose content of the perivitelline fluid and the permeability characteristics of the eggshell, are influential in hatching and are also important for the survival of dormant, unhatched juveniles. In this review, Roland Perry examines some attributes of the egg that are involved in dormancy and survival of nematodes and details the changes that occur during the hatching process.

Cranial ultrasound screening of preterm and term neonates

A cranial ultrasound examination was performed between 48 and 96 h of age on 580 neonates of 25-42 weeks gestation. The incidence of cerebroventricular haemorrhage (CVH) in infants less than 32 weeks gestation was 37%, compared with an incidence of 2.7% in infants of 32 weeks or more. The incidence of CVH unselected healthy term infants (between 37 and 42 weeks) was only 1.1%. Of the 13 infants of 32 weeks or more who were found to have a haemorrhage, nine had a small (Grade I) haemorrhage (69%) and none of these infants had abnormal neurological signs in the neonatal period. The remaining four infants with Grade II, III or IV haemorrhage developed either seizures or episodes of apnoea. Two of the 13 infants of 32 weeks or more with a haemorrhage died, one during the newborn period and the other at 5.5 months of age. CVH in asymptomatic infants of 32 weeks or more gestation is uncommon and does not justify routine cranial ultrasound scanning.

Egg-shell permeability and hatching of Ascaris suum

When eggs of Ascaris suum were transferred from glass-distilled water into 0.1--0.4 M NaCl solutions, the water content of the unhatched juveniles fell with increasing concentration of solute. The effect was reversible. The egg-shell was thus permeable to water. The osmotic pressure of the egg fluid was osmotically equivalent to between 0.1 and 0.2 M trehalose. In hatching experiments in Fairbairn's medium containing 0.1 or 0.2 M trehalose, only 5 and 3% respectively of the eggs hatched; 83% of the eggs hatched in the absence of trehalose. The evidence suggests that loss of solutes from the egg fluid permits an increase in the water content of the unhatched juveniles and that this may be responsible for ending their quiescence.