Insights from circulating microRNAs in cardiovascular entities in turner syndrome patients

CRELD1 variants are associated with bicuspid aortic valve in Turner syndrome

Turner syndrome (TS) is a chromosomal disorder caused by complete or partial loss of the second sex chromosome and exhibits phenotypic heterogeneity, even after accounting for mosaicism and karyotypic variation. Congenital heart defects (CHD) are found in up to 45 percent of girls with TS and span a phenotypic continuum of obstructive left-sided lesions, with bicuspid aortic valve (BAV) being the most common. Several recent studies have demonstrated a genome-wide impact of X chromosome haploinsufficiency, including global hypomethylation and altered RNA expression. The presence of such broad changes to the TS epigenome and transcriptome led others to hypothesize that X chromosome haploinsufficiency sensitizes the TS genome, and several studies have demonstrated that a second genetic hit can modify disease susceptibility in TS. The objective of this study was to determine whether genetic variants in known heart developmental pathways act synergistically in this setting to increase the risk for CHD, specifically BAV, in TS. We analyzed 208 whole exomes from girls and women with TS and performed gene-based variant enrichment analysis and rare-variant association testing to identify variants associated with BAV in TS. Notably, rare variants in CRELD1 were significantly enriched in individuals with TS who had BAV compared to those with structurally normal hearts. CRELD1 is a protein that functions as a regulator of calcineurin/NFAT signaling, and rare variants in CRELD1 have been associated with both syndromic and non-syndromic CHD. This observation supports the hypothesis that genetic modifiers outside the X chromosome that lie in known heart development pathways may influence CHD risk in TS.

The Changing Face of Turner Syndrome

Turner syndrome (TS) is a condition in females missing the second sex chromosome (45,X) or parts thereof. It is considered a rare genetic condition and is associated with a wide range of clinical stigmata, such as short stature, ovarian dysgenesis, delayed puberty and infertility, congenital malformations, endocrine disorders, including a range of autoimmune conditions and type 2 diabetes, and neurocognitive deficits. Morbidity and mortality are clearly increased compared with the general population and the average age at diagnosis is quite delayed. During recent years it has become clear that a multidisciplinary approach is necessary toward the patient with TS. A number of clinical advances has been implemented, and these are reviewed. Our understanding of the genomic architecture of TS is advancing rapidly, and these latest developments are reviewed and discussed. Several candidate genes, genomic pathways and mechanisms, including an altered transcriptome and epigenome, are also presented.

Expression profiling analysis reveals key microRNA-mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

Background

Patients with transposition of the great arteries (TGA) have different connected systemic chambers and this determines the long-term morbidities and survival. Limited findings have been reported to systematically identify miRNA and mRNA expression levels in such cohorts of patients. In this study, we aimed to characterize miRNAs, mRNAs, and miRNA-mRNA interaction networks in patients with TGA, with a systemic left (LV) and right ventricle (RV).

Materials and methods

Large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 TGA-RV patients, 16 TGA-LV patients, and 16 age and gender-matched controls. Using real-time quantitative PCR (RT-qPCR), the differential expression level of a single miRNA was validated. Enrichment analyses of altered miRNA and mRNA expression levels were identified using bioinformatics tools.

Results

Altered miRNA and mRNA expression levels were observed between TGA-RV and TGA-LV patients, together or separated, compared to controls. Among the deregulated miRNAs and mRNAs, 39 and 101 miRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Furthermore, 51 miRNAs were identified as significantly differentially expressed in patients with TGA-RV when compared to patients with TGA-LV. RT-qPCR relative expression level was highly consistent with microarray analysis results. Similarly, 36 and 164 mRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Additionally, miR-140-3p showed a higher expression level in patients with overt heart failure (FC = 1.54; P = 0.001) and miR-502-3p showed a higher expression level in patients died due to cardiac death (FC = 1.41; P = 0.011). Integrative analysis resulted in 21 and 23 target genes with higher and lower expression levels, respectively (r ≥ 0.50 and P < 0.05). These target genes (i.e., 21 and 23 target genes) showed an inverse direction of regulation with miRNA and exhibited a miRNA binding site position within the 3'UTR of the target gene.

Conclusion

Our findings provide new insights into a potential molecular biomarker(s) for patients with TGA that may guide better risk stratification and the development of novel targeting therapies. Future studies are needed to investigate the potential significance of miRNAs and mRNAs in TGA-related cardiovascular diseases.

MicroRNA-126-3p/5p and Aortic Stiffness in Patients with Turner Syndrome

Background: Turner Syndrome (TS) is a relatively rare X-chromosomal disease with increased cardiovascular morbidity and mortality. This study aimed to identify whether the circulating miR-126-3p/5p are involved in the pathophysiology of vascular dysfunction in TS. Methods: Using the RT-qPCR, the abundance levels of miR-126-3p and miR-126-5p were determined in 33 TS patients and 33 age-matched healthy volunteers (HVs). Vascular screening, including the assessment of blood pressure, pulse wave velocity, augmentation index, aortic deformation, arterial distensibility, and arterial elastance, was conducted in TS patients and HVs. Results: The abundance levels of miR-126-3p and miR-126-5p were significantly higher in TS patients compared to HVs (p < 0.0001). Within the TS cohort, miR-126-3p/5p correlated significantly with aortic deformation (r = 0.47, p = 0.01; r = 0.48, p < 0.01) and arterial distensibility (r = 0.55, p < 0.01; r = 0.48, p < 0.01). In addition, a significant negative correlation was demonstrated between miR-126-3p and arterial elastance (r = −0.48, p = 0.01). The receiver operating characteristic analysis showed that miR-126-3p and miR-126-5p separated the tested groups with high sensitivity and specificity. Conclusions: The abundance levels of miR-126-3p and miR-126-5p were significantly higher in TS patients compared to HVs. Within the TS cohort, a lower abundance level of miR-126-3p and miR-126-5p was linked with a significantly higher aortic stiffness.

Turner Syndrome

Turner syndrome (TS) affects approximately 1 out of every 1500–2500 live female births, with clinical features including short stature, premature ovarian failure, dysmorphic features and other endocrine, skeletal, cardiovascular, renal, gastrointestinal and neurodevelopmental organ system involvement. TS, a common genetic syndrome, is caused by sex chromosome aneuploidy, mosaicism or abnormalities with complete or partial loss of function of the second X chromosome. Advances in genetic and genomic testing have further elucidated other possible mechanisms that contribute to pathogenic variability in phenotypic expression that are not necessarily explained by monosomy or haploinsufficiency of the X chromosome alone. The role of epigenetics in variations of gene expression and how this knowledge can contribute to more individualized therapy is currently being explored. TS is established as a multisystemic condition, with several endocrine manifestations of TS affecting growth, puberty and fertility having significant impact on quality of life. Treatment guidelines are in place for the management of these conditions; however, further data on optimal management is needed.

MicroRNA-183-3p Is a Predictor of Worsening Heart Failure in Adult Patients With Transposition of the Great Arteries and a Systemic Right Ventricle

Aim: MicroRNAs (miRNAs) have been shown to play an important role in the progression of heart failure (HF). The aim of our study was to analyze miRNAs in the blood of patients with transposition of the great arteries and a systemic right ventricle (TGA-RV) in order to identify those that predict worsening HF.

Materials and Methods: In 36 patients with TGA-RV, SurePrint™ 8 × 60K Human v21 miRNA microarrays were used to determine the miRNA abundance profiles and compared to 35 age- and gender-matched healthy volunteers (HVs). MiRNAs that were most significantly abundant or best related to worsening HF were further validated by RT-qPCR.

Results: Using miRNA array analysis, a total of 50 down-regulated and 56 up-regulated miRNAs were found to be differentially abundant in TGA-RV patients compared to HVs. Six of these 106 miRNAs were significantly related to worsening HF. After validation by RT-qPCR, four miRNAs turned out to be significantly associated with worsening HF, namely miR-150-5p, miR-1255b-5p, miR-423-3p, and miR-183-3p. In the stepwise multivariable Cox regression analysis, ejection fraction of the systemic RV, high sensitive TNT and miR-183-3p were found to be independent predictors of worsening HF (P = 0.001, P = 0.002, and P = 0.001, respectively).

Conclusions: In patients with TGA-RV, miR-183-3p is an independent predictor of worsening HF and thus may be used as additional biomarker in the risk assessment of these patients.

Characterization of micro-RNA in women with different ovarian reserve

Women undergoing infertility treatment are routinely subjected to one or more tests of ovarian reserve. Therefore, an adequate assessment of the ovarian reserve is necessary for the treatment. In this study, we aimed to characterize the potential role of microRNAs (miRNAs) as biomarkers for women with different ovarian reserves. A total of 159 women were recruited in the study and classified according to their anti-Müllerian hormone (AMH) level into three groups: (1) low ovarian reserve (LAMH, n = 39), (2) normal ovarian reserve (NAMH, n = 80), and (3) high ovarian reserve (HAMH, n = 40). SurePrint Human miRNA array screening and reverse transcription-quantitative PCR (RT-qPCR) were respectively employed to screen and validate the miRNA abundance level in the three tested groups. Compared with NAMH, the abundance level of 34 and 98 miRNAs was found to be significantly altered in LAMH and HAMH, respectively. The abundance level of miRNAs was further validated by RT-qPCR in both, the screening samples as well as in an independent set of validation samples. The abundance levels of the validated miRNAs were significantly correlated with the AMH level. The best AUC value for the prediction of the increase and decrease in the AMH level was obtained for the miR-100-5p and miR-21-5p, respectively. The level of miRNAs abundance correlates with the level of AMH, which may serve as a tool for identifying women with a different ovarian reserve and may help to lay the ground for the development of novel diagnostic approaches.

Sex bias miRNAs in Cynoglossus semilaevis could play a role in transgenerational inheritance

Alterations of non-coding RNA profiling in spermatozoa are candidate mechanisms related to changes in paternal environment and progeny. Transgenerational inheritance of sex in pseudomales of Cynoglossus semilaevis, a fish with significant sex dimorphism, is a typical example of non-Mendelian inheritance. In the present study, miRNA profiles of spermatozoa were compared between male and pseudomale of C. semilaevis. Differential miRNAs in sperm from F0 and F1 generation also provides clues for revealing the possible role of non-coding RNA mediated transgenerational inheritance. Four sexual bias miRNAs, dre-miR-26a-5p, dre-miR-27b-3p, dre-miR-125b-5p,pol-199a-5p, were identified and verified in F0 and F1 generation of C. semilaevis. All of them were highly expressed in male sperm compared with pseudomale sperm. Function of target genes indicates that target genes of these differential RNAs are highly correlated with sex differentiation, gametogenesis and maintenance of secondary sexual characteristics. In a word, identification of epigenetic markers in gametes has great prospects in predicting susceptibility and properties in offsprings, and providing an indicator of parentalgenetic property.

Recurrent Neural Networks to Automatically Identify Rare Disease Epidemiologic Studies from PubMed

Rare diseases affect between 25 and 30 million people in the United States, and understanding their epidemiology is critical to focusing research efforts. However, little is known about the prevalence of many rare diseases. Given a lack of automated tools, current methods to identify and collect epidemiological data are managed through manual curation. To accelerate this process systematically, we developed a novel predictive model to programmatically identify epidemiologic studies on rare diseases from PubMed. A long short-term memory recurrent neural network was developed to predict whether a PubMed abstract represents an epidemiologic study. Our model performed well on our validation set (precision = 0.846, recall = 0.937, AUC = 0.967), and obtained satisfying results on the test set. This model thus shows promise to accelerate the pace of epidemiologic data curation in rare diseases and could be extended for use in other types of studies and in other disease domains.

Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein's Anomaly

Little is known about abundance level changes of circulating microRNAs (miRNAs) and messenger RNAs (mRNA) in patients with Ebstein’s anomaly (EA). Here, we performed an integrated analysis to identify the differentially abundant miRNAs and mRNA targets and to identify the potential therapeutic targets that might be involved in the mechanisms underlying EA. A large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 EA patients and 16 age and gender-matched healthy control volunteers (HVs). Differential abundance level of single miRNA and mRNA was validated by Real-Time quantitative PCR (RT-qPCR). Enrichment analyses of altered miRNA and mRNA abundance levels were identified using bioinformatics tools. Altered miRNA and mRNA abundance levels were observed between EA patients and HVs. Among the deregulated miRNAs and mRNAs, 76 miRNAs (49 lower abundance and 27 higher abundance, fold-change of ≥2) and 29 mRNAs (25 higher abundance and 4 lower abundance, fold-change of ≥1.5) were identified in EA patients compared to HVs. Bioinformatics analysis identified 37 pairs of putative miRNA-mRNA interactions. The majority of the correlations were detected between the lower abundance level of miRNA and higher abundance level of mRNA, except for let-7b-5p, which showed a higher abundance level and their target gene, SCRN3, showed a lower abundance level. Pathway enrichment analysis of the deregulated mRNAs identified 35 significant pathways that are mostly involved in signal transduction and cellular interaction pathways. Our findings provide new insights into a potential molecular biomarker(s) for the EA that may guide the development of novel targeting therapies.

MiR-340-3p-HUS1 axis suppresses proliferation and migration in lung adenocarcinoma cells

AIMS

The functions and molecular mechanisms of miR-340-3p in lung adenocarcinoma (LUAD) progression remain unclear. On the other hand, the role of HUS1 in LUAD progression should be further explored.

MAIN METHODS

Data from cancer database were subjected to bioinformatics analysis. Quantitative real-time PCR and western blot were performed to detect gene expression. Colony formation and MTT assay were performed to examine cell growth in vitro. Wound healing assays and transwell assays were performed to examine cell migration.

KEY FINDINGS

Here, our results showed that miR-340-3p was lower expressed in LUAD tissues and LUAD-derived cell lines. And miR-340-3p suppressed the proliferation and migration ability of LUAD cells. Further, miR-340-3p inhibits HUS1 expression, which was higher expressed in LUAD tissues and promoted the proliferation and migration ability of LUAD cells. Moreover, higher HUS1 expression was associated with poor survival rate and shorter survival time in patients with LUAD, and HUS1 expression was negative correlated with that of miR-340-3p in clinical samples. In addition, overexpression of HUS1 counteracted the downregulation of cell growth by miR-340-3p.

SIGNIFICANCE

The study mainly indicated that miR-340-3p may play a tumor suppressor role in the progression of LUAD, with the function of restraining HUS1 expression, highlighting a potential therapeutic target for LUAD.

MicroRNA-29b/c-3p Indicate Advanced Liver Fibrosis/Cirrhosis in Univentricular Heart Patients With and Without Fontan Palliation

Aim: The present study aims to identify those microRNAs (miRNAs) in patients with univentricular heart (UVH) disease with and without Fontan palliation that may be associated with advanced liver fibrosis/cirrhosis. Materials and Methods: SurePrint™ 8 × 60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles in the blood of 48 UVH patients with and without Fontan palliation and 32 matched healthy controls. The abundance levels of selected miRNAs have been validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Results: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-29b-3p and miR-29c-3p were significantly related to the model of end-stage liver disease (MELD)-Albumin and albumin-bilirubin (ALBI) score representing advanced liver fibrosis/cirrhosis. Relative expression levels of both miRNAs were significantly higher in patients with a higher collapsibility index representing venous hepatic congestion, a higher MELD-Albumin or ALBI score and incomplete or no Fontan palliation. In the logistic regression analysis, a MELD-Albumin score ≥ 11 or ALBI score > -2.6 were best predicted by total bilirubin (OR 6.630, P = 0.016), albumin (OR 0.424, P = 0.026), and miR-29c-3p (OR 33.060, P = 0.047). After adjustment to the status of Fontan palliation, however, no statistical significance of these parameters was found thus underlining the importance of palliation status on progression of liver fibrosis/ cirrhosis in UVH patients. Conclusions: In UVH patients with and without Fontan palliation, miR-29b-3p and miR-29c-3p seem to be markers of advanced liver fibrosis/cirrhosis and thus may be used in the risk assessment of these patients.