Comparative Analysis of Gammaherpesvirus Circular RNA Repertoires: Conserved and Unique Viral Circular RNAs.

Recent studies have identified circular RNAs (circRNAs) expressed from the Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV) human DNA tumor viruses. To gain initial insights into the potential relevance of EBV circRNAs in virus biology and disease, we assessed the circRNAome of the interspecies homologue rhesus macaque lymphocryptovirus (rLCV) in a naturally occurring lymphoma from a simian immunodeficiency virus (SIV)-infected rhesus macaque. This analysis revealed rLCV orthologues of the latency-associated EBV circular RNAs circRPMS1_E4_E3a and circEBNA_U. Also identified in two samples displaying unusually high lytic gene expression was a novel rLCV circRNA that contains both conserved and rLCV-specific RPMS1 exons and whose backsplice junctions flank an rLCV lytic origin of replication (OriLyt). Analysis of a lytic infection model for the murid herpesvirus 68 (MHV68) rhadinovirus identified a cluster of circRNAs near an MHV68 lytic origin of replication, with the most abundant of these, circM11_ORF69, spanning the OriLyt. Lastly, analysis of KSHV latency and reactivation models revealed the latency associated circRNA originating from the vIRF4 gene as the predominant viral circRNA. Together, the results of this study broaden our appreciation for circRNA repertoires in the Lymphocryptovirus and Rhadinovirus genera of gammaherpesviruses and provide evolutionary support for viral circRNA functions in latency and viral replication.IMPORTANCE Infection with oncogenic gammaherpesviruses leads to long-term viral persistence through a dynamic interplay between the virus and the host immune system. Critical for remodeling of the host cell environment after the immune responses are viral noncoding RNAs that modulate host signaling pathways without attracting adaptive immune recognition. Despite the importance of noncoding RNAs in persistent infection, the circRNA class of noncoding RNAs has only recently been identified in gammaherpesviruses. Accordingly, their roles in virus infection and associated oncogenesis are unknown. Here we report evolutionary conservation of EBV-encoded circRNAs determined by assessing the circRNAome in rLCV-infected lymphomas from an SIV-infected rhesus macaque, and we report latent and lytic circRNAs from KSHV and MHV68. These experiments demonstrate utilization of the circular RNA class of RNAs across 4 members of the gammaherpesvirus subfamily, and they identify orthologues and potential homoplastic circRNAs, implying conserved circRNA functions in virus biology and associated malignancies.

The Epstein Barr virus circRNAome.

Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs as well as the more recent discovery of over a hundred new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified EBV encoded circular RNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U fragment exon, and from the latency long non-coding RPMS1 locus. In addition, we identified circular RNAs expressed during reactivation including backsplicing from exon 8 to exon 2 of the LMP2 gene and a highly expressed circular RNA derived from intra-exonic backsplicing within the BHLF1 gene. While expression of most of these circular RNAs was found to depend on the EBV transcriptional program utilized and the transcription levels of the associated loci, expression of LMP2 exon 8 to exon 2 circular RNA was found to be cell model specific. Altogether we identified over 30 unique EBV circRNAs candidates and we validated and determined the structural features, expression profiles and nuclear/cytoplasmic distributions of several predominant and notable viral circRNAs. Further, we show that two of the EBV circular RNAs derived from the RPMS1 locus are detected in EBV positive clinical stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circular RNAs and it provides an essential foundation and resource for investigations into the functions and roles of this new class of EBV transcripts in EBV biology and diseases.

Single-Nucleotide Polymorphisms and Markers of Oxidative Stress in Healthy Women.

PURPOSE: There is accumulating evidence that oxidative stress is an important contributor to carcinogenesis. We hypothesized that genetic variation in genes involved in maintaining antioxidant/oxidant balance would be associated with overall oxidative stress. METHODS: We examined associations between single nucleotide polymorphisms (SNPs) in MnSOD, GSTP1, GSTM1, GPX1, GPX3, and CAT genes and thiobarbituric acid-reactive substances (TBARS), a blood biomarker of oxidative damage, in healthy white women randomly selected from Western New York (n = 1402). We used general linear models to calculate age-adjusted geometric means of TBARS across the variants. We also examined the associations within strata of menopausal status. RESULTS: For MnSOD, being heterozygous was associated with lower geometric means of TBARS (less oxidative stress), 1.28 mg/dL, compared to homozygous T-allele or homozygous C-allele,1.35 mg/dL, and 1.31 mg/dL correspondingly (p for trend = 0.01). This difference remained among postmenopausal women, 1.40 mg/dL for TT, 1.32 mg/dL for TC, and 1.34mg/dL for CC (p for trend 0.015); it was attenuated among premenopausal women. SNPs in the other genes examined (GSTP1, GSTM1, GPX1, GPX3, and CAT) were not associated with TBARS. CONCLUSIONS: Our findings suggest that genetic variation in MnSOD gene may be associated with oxidative status, particularly among postmenopausal women.

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.

Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC). Although previous investigations provide a strong link between EBV and gastric carcinomas, these studies were performed using selected EBV gene probes. Using a cohort of gastric carcinoma RNA-seq data sets from The Cancer Genome Atlas (TCGA), we performed a quantitative and global assessment of EBV gene expression in gastric carcinomas and assessed EBV associated cellular pathway alterations. EBV transcripts were detected in 17% of samples but these samples varied significantly in EBV coverage depth. In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads. Expression of LMP2, and to a lesser extent, LMP1 were also observed as was evidence of abortive lytic replication. Analysis of cellular gene expression indicated significant immune cell infiltration and a predominant IFNG response in samples expressing high levels of EBV transcripts relative to samples expressing low or no EBV transcripts. Despite the apparent immune cell infiltration, high levels of the cytotoxic T-cell (CTL) and natural killer (NK) cell inhibitor, IDO1, was observed in the hiEBVaGCs samples suggesting an active tolerance inducing pathway in this subgroup. These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry. Lastly, a panel of tumor suppressors and candidate oncogenes were expressed at lower levels in hiEBVaGC versus EBV-low and EBV-negative gastric cancers suggesting the direct regulation of tumor pathways by EBV.

Sympathetic activation increases NO release from eNOS but neither eNOS nor nNOS play an essential role in exercise hyperemia in the human forearm.

Nitric oxide (NO) release from endothelial NO synthase (eNOS) and/or neuronal NO synthase (nNOS) could be modulated by sympathetic nerve activity and contribute to increased blood flow after exercise. We examined the effects of brachial-arterial infusion of the nNOS selective inhibitor S-methyl-l-thiocitrulline (SMTC) and the nonselective NOS inhibitor N(G)-monomethyl-l-arginine (l-NMMA) on forearm arm blood flow at rest, during sympathetic activation by lower body negative pressure, and during lower body negative pressure immediately after handgrip exercise. Reduction in forearm blood flow by lower body negative pressure during infusion of SMTC was not significantly different from that during vehicle (-28.5 ± 4.02 vs. -34.1 ± 2.96%, respectively; P = 0.32; n = 8). However, l-NMMA augmented the reduction in forearm blood flow by lower body negative pressure (-44.2 ± 3.53 vs. -23.4 ± 5.71%; n = 8; P < 0.01). When lower body negative pressure was continued after handgrip exercise, there was no significant effect of either l-NMMA or SMTC on forearm blood flow immediately after low-intensity exercise (P = 0.91 and P = 0.44 for l-NMMA vs. saline and SMTC vs. saline, respectively; each n = 10) or high-intensity exercise (P = 0.46 and P = 0.68 for l-NMMA vs. saline and SMTC vs. saline, respectively; each n = 10). These results suggest that sympathetic activation increases NO release from eNOS, attenuating vasoconstriction. Dysfunction of eNOS could augment vasoconstrictor and blood pressure responses to sympathetic activation. However, neither eNOS nor nNOS plays an essential role in postexercise hyperaemia, even in the presence of increased sympathetic activation.

Development and validation of the fractional flow reserve (FFR) angiographic scoring tool (FAST) to improve the angiographic grading and selection of intermediate lesions that require FFR assessment.

BACKGROUND: Visual angiographic assessment of intermediate coronary lesions is poor at determining the functional significance. We sought to identify independent clinical and angiographic parameters associated with stenosis functional significance and applied them in a weighted fractional flow reserve angiographic scoring tool (FAST) to improve intermediate lesion selection for fractional flow reserve (FFR) assessment. METHODS AND RESULTS: Data from 100 patients with intermediate lesions previously assessed by FFR were retrospectively analyzed, and four independent variables that predicted FFR of less than or equal to 0.8 were identified: quantitative coronary angiography percent diameter stenosis [odds ratio (OR) 1.22, P<0.001], length more than 20 mm (OR 7.6, P=0.004), stenosis haziness (OR 16.6, P=0.005), and multivessel disease (OR 7.8, P=0.019). Applying these variables into the FAST score, we prospectively assessed a further 109 intermediate lesions (prevalence of FFR ≤0.8 was 29% in this validation cohort) and found that FAST was highly discriminative, predicting an FFR of less than or equal to 0.8 with a c-statistic of 0.865 (95% confidence interval 0.793-0.937, P<0.0001). At the optimal cutoff value, FAST score of more than 2 had a negative predictive value of 96.5% and a sensitivity of 93.8%. It would have reduced the pressure wire usage in the validation cohort by 52.3% (57 out of 109 cases), with only two false negatives and associated cost savings. CONCLUSION: The FAST score is a simple angiographic assessment tool for intermediate lesions that comprises four angiographic variables. A score of 2 or lower indicates low likelihood of lesion hemodynamic significance.

Single-nucleotide polymorphisms in DNA repair genes and association with breast cancer risk in the web study.

Base excision repair (BER) and nucleotide excision repair (NER) pathways repair damaged DNA, and polymorphisms in these genes might affect breast cancer susceptibility. We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ERCC4 rs1799801, XPC rs2227998, rs2228001, rs2228000, OGG1 rs1052133 and XRCC1 rs25487 and rs25486) and breast cancer risk, examining modification by smoking and alcohol consumption, using data from the Western New York Exposures and Breast Cancer Study. Women aged 35-79 years with incident breast cancer (n = 1170) and age- and race-matched controls (n = 2115) were enrolled. Genotyping was performed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Unconditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CIs). No significant associations were observed in premenopausal women. Among postmenopausal women, rs25487 and rs25486 (OR = 1.24; 95% CI 1.01-1.51 and OR = 1.23; 95% CI 1.01-1.49, respectively, for combined heterozygous and homozygous variant compared with reference) were associated with increased risk of breast cancer. Postmenopausal women carrying the variant allele of the synonymous XPC polymorphism (rs2227998) were also at borderline significantly increased risk (OR = 1.24; 95% CI 1.01-1.52, heterozygous variant compared with reference; OR = 1.22; 95% CI 1.01-1.48, for combined heterozygous and homozygous variant compared with reference). There was no evidence of genotype-smoking and genotype-alcohol consumption interactions for pre- and postmenopausal women. These results indicate that some of the variants in BER and NER genes may influence risk of postmenopausal breast cancer.

Atherosclerotic renal artery stenosis: review of pathophysiology, clinical trial evidence, and management strategies.

Renal artery stenosis is prevalent and commonly encountered by cardiovascular specialists. Recently published randomized studies have provoked tremendous controversies in the treatment strategy with regard to renal artery stenting. However, these studies are inconclusive because of major study limitations. As such, cardiovascular specialists are uncertain of the indications or utility of renal revascularization, with differing opinions on management by nephrologists and cardiologists. A greater understanding of this disease process, especially with regard to its functional significance and consequence and treatment strategies based on well-designed clinical trials, is sorely needed. Our review focuses on atherosclerotic renal artery stenosis, with an emphasis on indications for revascularization and review of current trial data.

Fame comes at a cost: a Canadian analysis of procedural costs in use of pressure wire to guide multivessel percutaneous coronary intervention.

The FAME-study authors claimed that fractional flow reserve (FFR)-guided multivessel percutaneous coronary intervention (PCI) achieved superior clinical outcome and lower cost compared with no FFR. However, patients were intended to undergo multivessel PCI with drug eluting stents prior to randomization, which tipped the cost-analysis heavily in favour of FFR. We retrospectively evaluated 100 intermediate coronary lesions assessed by FFR, and determined whether to perform PCI based on visual angiographic assessment alone. We found that angiographic-guided treatment underestimated functional significance of intermediate lesions, resulting in fewer implanted stents compared to FFR guidance. This, in addition to the pressure wire cost, increased procedural expenditure 2- to 3-fold when using FFR-guidance.

Physical activity and reduced breast cancer risk: a multinational study.

We evaluated the association between physical activity and breast cancer risk among 1,463 breast cancer cases and 4,862 controls in a multinational study. All subjects were asked how many times and for how long they exercised or engaged in strenuous physical labor per week. We used multivariate logistic regression to assess the association between physical activity and breast cancer risk. For all subjects combined, the multivariate-adjusted odds ratio was 50% lower (95% confidence interval = 0.4-0.6) for women who reported physical activity once per week or more after adjusting for age, race, body mass index, and pack years of smoking compared to those who reported physical activity less than once per week. Women who reported physical activity 3 times/wk or more did not gain any additional reduced risk. The amount of time spent in physical activity per session was also significantly associated with reduced risk. All ethnic groups examined including Caucasian-Americans, African-Americans, Hispanic-Americans, Tunisian-Arabs, and Polish-Caucasians were at 35% or greater reduced risk for breast cancer if they were physically active for more than 30 minutes per week. Our study shows that physical activity may reduce breast cancer risk regardless of race, weight category, or family history of breast cancer.

Effects of neuronal nitric oxide synthase on human coronary artery diameter and blood flow in vivo.

BACKGROUND: Nitric oxide (NO)-mediated local regulation of vascular tone is considered to involve endothelial NO synthase (eNOS). However, we recently reported that human forearm basal microvascular tone in vivo is tonically regulated by neuronal NO synthase (nNOS), in contrast to an acetylcholine-stimulated reduction in tone, which is eNOS dependent. Here, we investigated the in vivo effects of an nNOS-selective inhibitor, S-methyl-L-thiocitrulline (SMTC), on the human coronary circulation and on flow-mediated dilatation in the forearm. METHODS AND RESULTS: In patients with angiographically normal coronary arteries, intracoronary infusion of SMTC (0.625 micromol/min) reduced basal coronary blood flow by 34.1+/-5.2% (n=10; P<0.01) and epicardial coronary diameter by 3.6+/-1.2% (P=0.02) but had no effect on increases in flow evoked by intracoronary substance P (20 pmol/min). The nonselective NOS inhibitor N(G)-monomethyl-L-arginine (25 micromol/min) also reduced basal coronary flow (by 22.3+/-5.3%; n=8; P<0.01) but, in contrast to SMTC, inhibited substance P-induced increases in flow (P<0.01). In healthy volunteers, local infusion of SMTC (0.2 micromol/min) reduced radial artery blood flow by 36.0+/-6.4% (n=10; P=0.03) but did not affect flow-mediated dilatation (P=0.55). In contrast, N(G)-monomethyl-L-arginine (2 micromol/min) infusion reduced radial blood flow to a similar degree (by 39.7+/-11.8%; P=0.02) but also inhibited flow-mediated dilatation by approximately 80% (P<0.01). CONCLUSIONS: These data indicate that local nNOS-derived NO regulates basal blood flow in the human coronary vascular bed, whereas substance P-stimulated vasodilatation is eNOS mediated. Thus, nNOS and eNOS have distinct local roles in the physiological regulation of human coronary vascular tone in vivo.

Neuronal nitric oxide synthase and human vascular regulation.

Vascular blood flow and its distribution among different vascular beds are regulated by changes in microvascular tone. Nitric oxide (NO) plays a key role in the local paracrine regulation of vessel tone both under resting conditions and when blood flow increases in response to agonist stimulation or increased shear stress. The conventional notion that endothelial NO synthase (eNOS)-derived NO is largely responsible for both effects has been challenged by first-in-human studies with a selective inhibitor of neuronal NOS (nNOS), S-methyl-l-thiocitrulline (SMTC). These studies reveal that SMTC causes a reduction in basal blood flow in the normal human forearm and coronary circulations (that is reversed by l-arginine), without affecting the eNOS-mediated vasodilatation elicited by acetylcholine, substance P, or increased shear stress. S-methyl-l-thiocitrulline also inhibits mental stress-induced vasodilatation. These results are consistent with a significant body of experimental studies suggesting that nNOS plays an important role in the local regulation of vessel tone in other species, independent of the effects of nNOS-derived NO in the central nervous system. These emerging data suggest that eNOS and nNOS have distinct roles in the physiologic local regulation of human microvascular tone in vivo and pave the way for further detailed investigation of the relative contribution of nNOS and eNOS in vascular regulation in human disease.

Neuronal nitric oxide synthase regulates basal microvascular tone in humans in vivo.

BACKGROUND: Nitric oxide (NO) has a pivotal role in the regulation of vascular tone and blood flow, with dysfunctional release contributing to disease pathophysiology. These effects have been attributed to NO production by the endothelial NO synthase (eNOS); however, recent evidence suggests that a neuronal NO synthase (nNOS) may also be expressed in arterial vessels. METHODS AND RESULTS: We undertook a first-in-humans investigation of the role of nNOS in the local regulation of vascular blood flow in healthy subjects. Brachial artery infusion of the nNOS-specific inhibitor S-methyl-L-thiocitrulline (SMTC, 0.025 micromol/min to 0.2 micromol/min) caused a dose-dependent reduction in basal flow, with a 30.1+/-3.8% decrease at the highest dose (n=10; mean+/-SE; P<0.01). The effect of SMTC was abolished by coinfusion of the NO synthase substrate L-arginine but was unaffected by D-arginine. A similar reduction in basal flow with the nonselective NO synthase inhibitor N(G)-monomethyl-L-arginine (L-NMMA; 37.4+/-3.1%, n=10) required a 20-fold higher dose of 4 micromol/min. At doses that produced comparable reductions in basal flow, only L-NMMA (4 micromol/min) and not SMTC (0.2 micromol/min) inhibited acetylcholine-induced vasodilation; however, both SMTC and L-NMMA inhibited the forearm vasodilator response to mental stress. CONCLUSIONS: Basal forearm blood flow in humans is regulated by nNOS-derived NO, in contrast to the acetylcholine-stimulated increase in blood flow, which, as shown previously, is mediated primarily by eNOS. These data indicate that vascular nNOS has a distinct local role in the physiological regulation of human microvascular tone in vivo.

Low-volume hydrodynamic gene delivery to the rat liver via an isolated segment of the inferior vena cava: efficiency, cardiovascular response and intrahepatic vascular dynamics.

BACKGROUND: Clinical application of hydrodynamic gene delivery to the liver requires the use of small volumes, an evaluation of the cardiovascular consequences of acute volume overload, and a better understanding of the intrahepatic vascular pressures driving gene delivery. Injection of DNA solution into the isolated segment of inferior vena cava (IVC) draining the hepatic veins is a potentially valuable low-volume approach. METHODS: Various volumes of DNA solution (pGL3 plasmid) were injected at 100 ml/min either systemically or into the isolated IVC segment in the DA rat. Arterial pressure, portal venous pressure, heart rate and electrocardiogram, in addition to reporter gene expression in the liver, were monitored. RESULTS: The 2% volume was > 10 000-fold more effective when delivered via the IVC segment than when given systemically, and as effective as 6% systemically. Isolation of the IVC segment caused profound falls in arterial pressure, with electrocardiogram signs of myocardial ischemia. On release of the IVC ties, without DNA infusion (no volume overload), arterial pressure recovered rapidly. However, with DNA infusion (volume overload) there was a brief recovery of arterial pressure, followed by complete heart block and fall in arterial pressure and pulse for several minutes. Portal venous pressure rose steeply to 30-33 mm Hg during the infusion. CONCLUSIONS: The IVC segment approach enables excellent gene delivery to the whole liver with small volumes, but causes severe cardiovascular disturbances in the rat. Portal venous pressures are slightly higher than in the mouse, and suggest functional outflow obstruction by the capillary bed of the intestines.