Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells

Genome-wide association studies have identified >250 genetic variants associated with coronary artery disease (CAD), but the causal variants, genes and molecular mechanisms remain unknown at most loci. We performed pooled CRISPR screens to test the impact of sequences at or near CAD-associated genetic variants on vascular endothelial cell functions. Using CRISPR knockout, inhibition and activation, we targeted 1998 variants at 83 CAD loci to assess their effect on three adhesion proteins (E-selectin, ICAM1, VCAM1) and three key endothelial functions (nitric oxide and reactive oxygen species production, calcium signalling). At a false discovery rate ≤10%, we identified significant CRISPR perturbations near 42 variants located within 26 CAD loci. We used base editing to validate a putative causal variant in the promoter of the FES gene. Although a few of the loci include genes previously characterized in endothelial cells (e.g. AIDA, ARHGEF26, ADAMTS7), most are implicated in endothelial dysfunction for the first time. Detailed characterization of one of these new loci implicated the RNA helicase DHX38 in vascular endothelial cell senescence. While promising, our results also highlighted several limitations in using CRISPR perturbations to functionally dissect GWAS loci, including an unknown false negative rate and potential off-target effects.

The effects of simulated transportation conditions on the core body and extremity temperature, blood physiology, and behavior of white-strain layer pullets

Transportation of poultry is stressful. The transportation of broilers has been well studied, while the transportation of layer pullets from rearing to laying facilities has not been thoroughly evaluated. This experiment aimed to establish the effects of temperature (T)/RH combinations and duration (D) of transport, via a 5 × 2 factorial arrangement of simulated transport conditions using 5 T/RH combinations (21°C with 30% RH [21/30], 21°C with 80% RH [21/80], 30°C with 30% RH [30/30], 30°C with 80% RH [30/80], and -15°C with uncontrolled RH [-15]), and 2 exposure D (4 or 8 h). Pullets (18-19 wk; n = 240) were obtained from 3 commercial farms (N = 3 farms). Pretreatment, birds were orally administered a miniature data logger to record core body temperature (CBT), an initial blood sample was taken (5 birds/replicate), and initial foot T was recorded. Behavior during exposure was video recorded. Following exposure, a final blood sample was taken (analyzed for heterophil to lymphocyte ratio, partial pressure of CO₂, total CO₂, bicarbonate, and glucose), birds were slaughtered, and data loggers were retrieved. Data were analyzed as a randomized complete block design via Proc Mixed (SAS 9.4) and significance was declared at P ≤ 0.05. There were no interactions observed for the T/RH and D combinations throughout the study. The CBT and foot T were lowest in pullets exposed to -15 compared with all other treatments. Foot T was also highest in pullets exposed to 30/80 compared with -15, 21/30, and 21/80. There was no impact of T/RH on pullet blood physiology. Activity and thermoregulatory behaviors were impacted by the T/RH combinations. Pullets exposed to 30/30 and 30/80 spent the most time panting. Pullets exposed to 30/80 also spent the least amount of time motionless. Duration had minor impacts on pullet CBT, blood physiology, and behavior. These data indicate that as a response to thermal stress, layer pullets were successful at implementing mechanisms to maintain homeostasis.

The effects of simulated transport conditions on the muscle tissue characteristics of white-strain layer pullets

The objective of this study was to evaluate the effects of temperature (T)/relative humidity (RH) combinations and exposure duration (D) on the muscle tissue characteristics of layer pullets during simulated transport. While layer pullets are not processed for meat, muscle physiology can be used as an indicator to assess welfare. Pullets (n = 240) were randomly assigned to 1 of 5 T/RH combinations (-15°C uncontrolled RH [-15], 21°C 30%RH [21/30], 21°C 80%RH [21/80], 30°C 30%RH [30/30], and 30°C 80%RH [30/80]) and 2 D (4 or 8 h) in a 5 x 2 factorial arrangement (3 replications). Birds were weighed before exposure, crated (density 45.5 kg/m2) and exposed to the conditions above. After exposure, birds were weighed (live shrink calculated) and slaughtered using a small-scale facility. Postslaughter, carcasses were eviscerated, and an initial pH was obtained from the right breast and thigh. Final breast and thigh pH and color values (lightness [L∗], yellowness [b∗], and redness [a∗]) were obtained 30 h postslaughter. Left breast muscles were frozen and analyzed for thaw and cook loss 4 wk postslaughter. Data were analyzed as a randomized complete block design via ANOVA (Proc Mixed; SAS 9.4), with farm of origin as block. Differences were considered significant when P ≤ 0.05. Live shrink (kg) was higher for pullets exposed to 30/30 and 30/80 compared with those exposed to 21/80 (P = 0.04) and for pullets exposed for 8 h compared with 4 h (P < 0.01). Breast muscle thaw loss (%) was higher in pullets exposed for 4 h compared with 8 h (P = 0.01). Breast and thigh muscle a∗ were higher for pullets exposed to 30/30 compared with 21/30 (P = 0.02). Thigh muscle b∗ was lower for pullets exposed to -15 compared with 21/80 (P = 0.05). Breast b∗ was higher for pullets exposed for 8 h compared with 4 h (P = 0.04). The results from this study demonstrates that increasing exposure D had minor effects on pullet muscle characteristics. In addition, layer pullets coped well with thermal stressors associated with simulated transport.

Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene

BACKGROUND

Genome-wide association studies (GWAS) have identified hundreds of loci associated with coronary artery disease (CAD) and blood pressure (BP) or hypertension. Many of these loci are not linked to traditional risk factors, nor do they include obvious candidate genes, complicating their functional characterization. We hypothesize that many GWAS loci associated with vascular diseases modulate endothelial functions. Endothelial cells play critical roles in regulating vascular homeostasis, such as roles in forming a selective barrier, inflammation, hemostasis, and vascular tone, and endothelial dysfunction is a hallmark of atherosclerosis and hypertension. To test this hypothesis, we generate an integrated map of gene expression, open chromatin region, and 3D interactions in resting and TNFα-treated human endothelial cells.

RESULTS

We show that genetic variants associated with CAD and BP are enriched in open chromatin regions identified in endothelial cells. We identify physical loops by Hi-C and link open chromatin peaks that include CAD or BP SNPs with the promoters of genes expressed in endothelial cells. This analysis highlights 991 combinations of open chromatin regions and gene promoters that map to 38 CAD and 92 BP GWAS loci. We validate one CAD locus, by engineering a deletion of the TNFα-sensitive regulatory element using CRISPR/Cas9 and measure the effect on the expression of the novel CAD candidate gene AIDA.

CONCLUSIONS

Our data support an important role played by genetic variants acting in the vascular endothelium to modulate inter-individual risk in CAD and hypertension.

PHACTR1 splicing isoforms and eQTLs in atherosclerosis-relevant human cells

Background

Genome-wide association studies (GWAS) have identified a variant (rs9349379) at the phosphatase and actin regulator 1 (PHACTR1) locus that is associated with coronary artery disease (CAD). The same variant is also an expression quantitative trait locus (eQTL) for PHACTR1 in human coronary arteries (hCA). Here, we sought to characterize PHACTR1 splicing pattern in atherosclerosis-relevant human cells. We also explored how rs9349379 modulates the expression of the different PHACTR1 splicing isoforms.

Methods

We combined rapid amplification of cDNA ends (RACE) with next-generation long-read DNA sequencing to discover all PHACTR1 transcripts in many human tissues and cell types. We measured PHACTR1 transcripts by qPCR to identify transcript-specific eQTLs.

Results

We confirmed a brain-specific long transcript, a short transcript expressed in monocytes and four intermediate transcripts that are different due to alternative splicing of two in-frame exons. In contrast to a previous report, we confirmed that the PHACTR1 protein is present in vascular smooth muscle cells. In 158 hCA from our collection and the GTEx dataset, rs9349379 was only associated with the expression levels of the intermediate PHACTR1 transcripts.

Conclusions

Our comprehensive transcriptomic profiling of PHACTR1 indicates that this gene encodes six main transcripts. Five of them are expressed in hCA, where atherosclerotic plaques develop. In this tissue, genotypes at rs9349379 are associated with the expression of the intermediate transcripts, but not the immune-specific short transcript. This result suggests that rs9349379 may in part influence CAD by modulating the expression of intermediate PHACTR1 transcripts in endothelial or vascular smooth muscle cells found in hCA.

Electronic supplementary material

The online version of this article (10.1186/s12881-018-0616-7) contains supplementary material, which is available to authorized users.

Frameshift indels introduced by genome editing can lead to in-frame exon skipping

The introduction of frameshift indels by genome editing has emerged as a powerful technique to study the functions of uncharacterized genes in cell lines and model organisms. Such mutations should lead to mRNA degradation owing to nonsense-mediated mRNA decay or the production of severely truncated proteins. Here, we show that frameshift indels engineered by genome editing can also lead to skipping of “multiple of three nucleotides” exons. Such splicing events result in in-frame mRNA that may encode fully or partially functional proteins. We also characterize a segregating nonsense variant (rs2273865) located in a “multiple of three nucleotides” exon of LGALS8 that increases exon skipping in human erythroblast samples. Our results highlight the potentially frequent contribution of exonic splicing regulatory elements and are important for the interpretation of negative results in genome editing experiments. Moreover, they may contribute to a better annotation of loss-of-function mutations in the human genome.

Apolipoprotein D Transgenic Mice Develop Hepatic Steatosis through Activation of PPARγ and Fatty Acid Uptake

Transgenic mice (Tg) overexpressing human apolipoprotein D (H-apoD) in the brain are resistant to neurodegeneration. Despite the use of a neuron-specific promoter to generate the Tg mice, they expressed significant levels of H-apoD in both plasma and liver and they slowly develop hepatic steatosis and insulin resistance. We show here that hepatic PPARγ expression in Tg mice is increased by 2-fold compared to wild type (WT) mice. Consequently, PPARγ target genes Plin2 and Cide A/C are overexpressed, leading to increased lipid droplets formation. Expression of the fatty acid transporter CD36, another PPARgamma target, is also increased in Tg mice associated with elevated fatty acid uptake as measured in primary hepatocytes. Elevated expression of AMPK in the liver of Tg leads to phosphorylation of acetyl CoA carboxylase, indicating a decreased activity of the enzyme. Fatty acid synthase expression is also induced but the hepatic lipogenesis measured in vivo is not significantly different between WT and Tg mice. In addition, expression of carnitine palmitoyl transferase 1, the rate-limiting enzyme of beta-oxidation, is slightly upregulated. Finally, we show that overexpressing H-apoD in HepG2 cells in presence of arachidonic acid (AA), the main apoD ligand, increases the transcriptional activity of PPARγ. Supporting the role of apoD in AA transport, we observed enrichment in hepatic AA and a decrease in plasmatic AA concentration. Taken together, our results demonstrate that the hepatic steatosis observed in apoD Tg mice is a consequence of increased PPARγ transcriptional activity by AA leading to increased fatty acid uptake by the liver.

A cytosolic trans-activation domain essential for ammonium uptake

Polytopic membrane proteins are essential for cellular uptake and release of nutrients. To prevent toxic accumulation, rapid shut-off mechanisms are required. Here we show that the soluble cytosolic carboxy terminus of an oligomeric ammonium transporter from Arabidopsis thaliana serves as an allosteric regulator essential for function; mutations in the C-terminal domain, conserved between bacteria, fungi and plants, led to loss of transport activity. When co-expressed with intact transporters, mutants inactivated functional subunits, but left their stability unaffected. Co-expression of two inactive transporters, one with a defective pore, the other with an ablated C terminus, reconstituted activity. The crystal structure of an Archaeoglobus fulgidus ammonium transporter (AMT) suggests that the C terminus interacts physically with cytosolic loops of the neighbouring subunit. Phosphorylation of conserved sites in the C terminus are proposed as the cognate control mechanism. Conformational coupling between monomers provides a mechanism for tight regulation, for increasing the dynamic range of sensing and memorizing prior events, and may be a general mechanism for transporter regulation.

Development and use of fluorescent nanosensors for metabolite imaging in living cells

To understand metabolic networks, fluxes and regulation, it is crucial to be able to determine the cellular and subcellular levels of metabolites. Methods such as PET and NMR imaging have provided us with the possibility of studying metabolic processes in living organisms. However, at present these technologies do not permit measuring at the subcellular level. The cameleon, a fluorescence resonance energy transfer (FRET)-based nanosensor uses the ability of the calcium-bound form of calmodulin to interact with calmodulin binding polypeptides to turn the corresponding dramatic conformational change into a change in resonance energy transfer between two fluorescent proteins attached to the fusion protein. The cameleon and its derivatives were successfully used to follow calcium changes in real time not only in isolated cells, but also in living organisms. To provide a set of tools for real-time measurements of metabolite levels with subcellular resolution, protein-based nanosensors for various metabolites were developed. The metabolite nanosensors consist of two variants of the green fluorescent protein fused to bacterial periplasmic binding proteins. Different from the cameleon, a conformational change in the binding protein is directly detected as a change in FRET efficiency. The prototypes are able to detect various carbohydrates such as ribose, glucose and maltose as purified proteins in vitro. The nanosensors can be expressed in yeast and in mammalian cell cultures and were used to determine carbohydrate homeostasis in living cells with subcellular resolution. One future goal is to expand the set of sensors to cover a wider spectrum of metabolites by using the natural spectrum of bacterial periplasmic binding proteins and by computational design of the binding pockets of the prototype sensors.

A new subfamily of sucrose transporters, SUT4, with low affinity/high capacity localized in enucleate sieve elements of plants

A new subfamily of sucrose transporters from Arabidopsis (AtSUT4), tomato (LeSUT4), and potato (StSUT4) was isolated, demonstrating only 47% similarity to the previously characterized SUT1. SUT4 from two plant species conferred sucrose uptake activity when expressed in yeast. The K(m) for sucrose uptake by AtSUT4 of 11.6 +/- 0.6 mM was approximately 10-fold greater than for all other plant sucrose transporters characterized to date. An ortholog from potato had similar kinetic properties. Thus, SUT4 corresponds to the low-affinity/high-capacity saturable component of sucrose uptake found in leaves. In contrast to SUT1, SUT4 is expressed predominantly in minor veins in source leaves, where high-capacity sucrose transport is needed for phloem loading. In potato and tomato, SUT4 was immunolocalized specifically to enucleate sieve elements, indicating that like SUT1, macromolecular trafficking is required to transport the mRNA or the protein from companion cells through plasmodesmata into the sieve elements.

A new subfamily of sucrose transporters, SUT4, with low affinity/high capacity localized in enucleate sieve elements of plants

A new subfamily of sucrose transporters from Arabidopsis (AtSUT4), tomato (LeSUT4), and potato (StSUT4) was isolated, demonstrating only 47% similarity to the previously characterized SUT1. SUT4 from two plant species conferred sucrose uptake activity when expressed in yeast. The K(m) for sucrose uptake by AtSUT4 of 11.6 +/- 0.6 mM was approximately 10-fold greater than for all other plant sucrose transporters characterized to date. An ortholog from potato had similar kinetic properties. Thus, SUT4 corresponds to the low-affinity/high-capacity saturable component of sucrose uptake found in leaves. In contrast to SUT1, SUT4 is expressed predominantly in minor veins in source leaves, where high-capacity sucrose transport is needed for phloem loading. In potato and tomato, SUT4 was immunolocalized specifically to enucleate sieve elements, indicating that like SUT1, macromolecular trafficking is required to transport the mRNA or the protein from companion cells through plasmodesmata into the sieve elements.

Expression of a wheat ADP-glucose pyrophosphorylase gene during development of normal and water-stress-affected anthers

In wheat (Triticum aestivum L.), water deficit during meiosis in the microspore mother cells (MMCs) induces pollen abortion, resulting in the failure of fertilization and a reduction in grain set. In stressed plants, meiosis in MMCs proceeds normally but subsequent pollen development is arrested. Unlike normal pollen grains, which accumulate starch during the late maturation phase, stress-affected anthers contain pollen grains with little or no starch. Stress also alters the normal distribution of starch in the anther wall and connective tissue. To determine how starch biosynthesis is regulated within the developing anthers of stressed plants, we studied the expression of ADP-glucose pyrophosphorylase (AGP), which catalyzes the rate limiting step of starch biosynthesis. Two partial-length cDNAs corresponding to the large subunit of AGP were amplified by RT-PCR from anther RNA, and used as probes to monitor AGP expression in developing anthers of normal and water-stressed plants. These clones, WAL1 and WAL2, had identical deduced amino acid sequences and shared 96% sequence identity at the nucleic acid level. In normal anthers, AGP expression was biphasic, indicating that AGP expression is required for starch biosynthesis both during meiosis and later during pollen maturation. AGP expression in stressed anthers was not affected during the first phase of starch accumulation, but was strongly inhibited during the second phase. We conclude from these results that the reduced starch deposition later in the development of stressed pollen could be the result of a lower expression of AGP. However, this inhibition of AGP expression is unlikely to be the primary cause of male sterility because anatomical symptoms of pollen abortion are observed prior to the time when AGP expression is inhibited.

Induction of Male Sterility in Wheat by Meiotic-Stage Water Deficit Is Preceded by a Decline in Invertase Activity and Changes in Carbohydrate Metabolism in Anthers

Water deficit during meiosis in pollen mother cells of wheat (Triticum aestivum L.) induces male sterility, which can reduce grain set by 40 to 50%. In plants stressed during meiosis and then rewatered, division of pollen mother cells proceeds normally but subsequent pollen development is arrested 3 or 4 d later. An inhibition of starch accumulation within the pollen grain suggested that an alteration in carbohydrate metabolism or assimilate supply may be involved in pollen abortion. We measured levels of various carbohydrates and activities of key enzymes of Suc metabolism and starch synthesis at different stages of pollen development in anthers collected from well-watered and water-stressed plants. Compared to controls, soluble sugars increased in anthers stressed during meiosis, then decreased at later poststress stages. Sucrose and myoinositol accounted for part of the sugar accumulation. The activity of soluble acid invertase declined 4-fold during the stress period and never recovered thereafter. Sucrose synthase activity during starch accumulation in pollen was also lower in the anthers of plants stressed at meiosis. Stress had little negative effect on the activities of ADP-glucose pyrophosphorylase or soluble and granule-bound starch synthase during starch accumulation in pollen, although at the earlier stages, ADP-glucose pyrophosphorylase activity in stressed anthers was slightly lower compared to controls. The results suggest that carbohydrate starvation per se and inhibition of the enzymes of starch synthesis probably were not responsible for the stress-induced pollen abortion. Instead, an inability to metabolize incoming sucrose to hexoses may be involved in this developmental lesion.

Evidence against the Regulation of Grain Set by Spikelet Abscisic Acid Levels in Water-Stressed Wheat

A possible role of abscisic acid (ABA) in the regulation of grain set in water-stressed wheat (Triticum aestivum L.) was investigated using a split root system to dry half the roots while the remainder were kept watered. Water uptake by the wet roots maintained the leaf water potential at the normal level, whereas the ABA produced in the dry roots was transported to the spike. This caused the spikelet ABA level to increase to the same extent as when the entire root system was stressed to permit a drop in the leaf water potential. In spite of this, the former treatment did not induce a reduction in grain set, whereas the latter did. Thus, contrary to previous reports, water stress-induced changes in spikelet ABA level alone do not appear to regulate grain set.

Water-stress-induced ethylene production in wheat : a fact or artifact?

Effects of water stress on ethylene evolution from excised leaf segments and intact plants of wheat (Triticum aestivum L. cv Katepwa) were studied. Excised leaf segments of 8 day or 6 week old plants were dried until they lost 8% of their fresh weight (water potential about -2.3 megapascals). These and nondried control leaf segments (water potential about -1.0 megapascal) were sealed in glass tubes, and their ethylene production rates were compared by head space analysis via gas-chromatography. The dried leaves of both ages produced significantly more ethylene than the corresponding controls. However, when 6 week old intact plants were water-stressed by withholding water supply, and their ethylene production measured using a continuousflow system, no increase in ethylene was deteceted despite a drop in water potential to -2.9 megapascals over 6 days. Even the leaf segments excised from plants that had been subjected to water stress for 2, 4, or 6 days produced no more ethylene (in sealed tubes) than the leaves from well-watered plants. In fact, the ethylene production by these segments decreased with the increase in the severity of stress experienced by the plants. The results show that the commonly reported overproduction of ethylene by excised leaves subjected to rapid drying represents an artifact, which has little relevance to the water stress responses of intact wheat plants.

Influence of starvation on absorption, distribution, and action of barbital in mice and rats

The influence of food deprivation on the disposition of barbital during the early phase following administration of the drug was studied in mice and rats. Starvation consisted of withholding solid food, but not water, for 24–72 h in mice, and 72 h in rats. The results show that starvation leads to higher blood concentrations of barbital given intraperitoneally (i.p.) and subcutaneously to mice and rats, and intramuscularly to rats. This effect was observed 2.5–10 min following the injection of the barbiturate. In mice, starvation significantly reduced the interval between injection of the drug and loss of the righting reflex, but it extended the duration of the sleeping period. When barbital was given intravenously, starvation no longer resulted in higher blood concentrations of the drug, although starved mice went to sleep more rapidly than fed controls. At the moment of loss of the righting reflex. starved mice had significantly lower concentrations of barbital in the brain than fed controls. The total blood and plasma volumes of starved animals were moderately increased when expressed as a percentage of the body weight. These results suggest that starvation might influence the early phase of barbital absorption following its parenteral administration. There is also an indication that starvation could induce a state of hypersensitivity of the central nervous system to barbital.