Altered microRNAs expression levels of sperm and seminal plasma in patients with infertile ejaculates compared with normozoospermic males

Approximately 15% of couples are unable to conceive after one year of unprotected intercourse. Because sperm can be accessed with ease, it is reasonable to search for non-invasive biomarkers in semen. MicroRNAs are a family of short single-stranded non-coding RNA molecules that are capable of regulating gene expression and causing mRNA degradation. We studied the most common 11 spermatogenesis-related microRNAs expression levels in sperm and seminal plasma from patients with oligozoospermic or asthenozoospermic ejaculates, and in men with normozoospermic ejaculates. Five of these miRNAs were significantly upregulated and three were downregulated in infertile males compared to men with normozoospermic ejaculates. A statistically significant negative correlation was found between the sperm concentration and several microRNA expression level (let-7a, miR-7-1-3p, miR-141, miR-200a, and miR-429, p < 0.0001) both in sperm and in seminal plasma. We also found positive correlation between sperm concentration and some miRNA expression levels (miR-15b, miR-34b, and miR-122, p < 0.001) in sperm and in seminal plasma. This is the first study to demonstrate differences between sperm and seminal plasma miRNA expression level and to identify a correlation between the sperm concentration and miRNAs expression level. Therefore, these MiRNAs could have the potential be used as non-invasive biomarkers to diagnose males with impaired sperm production.

Laboratory biomarkers for lung disease severity and progression in cystic fibrosis

Although the clinical outcomes of cystic fibrosis (CF) have been markedly improved through the recent implementation of novel CF transmembrane conductance regulator (CFTR) modulator drugs, robust and reliable biomarkers are still demanded for the early detection of CF lung disease progression, monitoring treatment efficacy and predicting life-threatening clinical complications. Thus, there is an unmet need to identify and validate novel, ideally blood based biomarkers with strong correlations to the severity of CF lung disease, which represents a major contribution to overall CF morbidity and mortality. In this review, we aim to summarize the utility of thus far studied blood-, sputum- and bronchoalveolar lavage (BAL)-based biomarkers to evaluate inflammatory conditions in the lung and to follow treatment efficacy in CF. Measurements of sweat chloride concentrations and the spirometric parameter FEV₁ are currently utilized to monitor CFTR function and the effect of various CF therapies. Nonetheless, both have inherent pitfalls and limitations, thus routinely analyzed biomarkers in blood, sputum or BAL samples are required as surrogates for lung disorders. Recent discovery of new protein (e.g. HE4) and RNA-based biomarkers, such as microRNAs may offer a higher efficacy, which in aggregate may be valuable to evaluate disease prognosis and to substantiate CF drug efficacy.

Utilization of acute vascular imaging and neurointervention for acute ischaemic stroke patients in 20 Hungarian stroke centers

Background and purpose

Acute mortality rate of stroke in Hungary is significantly higher than in Western Europe, which is likely to be partially attributable to suboptimal treatment.

Methods

We examined the use of acute vascular imaging and mechanical thrombectomy for acute ischaemic stroke patients. We collected data on 20 consecutive patients from Hungarian stroke centers before 31st August 2016.

Results

Out of the reported 410 patients, 166 (40.4%) underwent CT angiography and 44 (10.7%) had mechanical thrombectomy.

Conclusion

Only about 1/3 of acute ischaemic stroke patients eligible for thrombectomy actually had it. The underlying reasons include long onset-to-door time, low utilization of acute vessel imaging and a limited neuro-intervention capacity needing improvement.

Copy number variants detection by microarray and multiplex ligation-dependent probe amplification in congenital heart diseases

Congenital heart diseases (CHDs) are the most common birth defects among life births, which could be presented as isolated or syndromic with other congenital malformations. The etiology of CHD largely unknown, genetic and environmental factors contribute to the disease. Recurrent copy number variants (CNVs) have been reported in the pathogenesis of CHD. The aim of this study was to evaluate the clinical utility of multiplex ligation-dependent probe amplification (MLPA) and microarray analyses on isolated and syndromic CHD cases and to explore the relationship between identified CNVs and CHD. Eighteen prenatal samples, 16 isolated and 33 syndromic patients with mild to severe CHD phenotype were tested. Prenatal and isolated CHD cases did not show pathogenic CNVs. Clinically significant CNVs were detected in 7/33 (21%) syndromic CHD patients: del 22q11.2 (n = 2), 8p23.1 duplication (n = 2), deletion 5p (n = 1), deletion 6q21q22 (n = 1), unbalanced translocation causing partial deletion of 4q34.3 and duplication of 6q25.1 (n = 1). These genomic imbalances contain genes that has been associated with human CHD before. The present study demonstrates that using microarray and MLPA analysis increase the detection rate of causal CNVs in individuals with syndromic CHD.

Human epididymis protein 4 (HE4) levels inversely correlate with lung function improvement (delta FEV1) in cystic fibrosis patients receiving ivacaftor treatment

BACKGROUND

We have recently shown that human epididymis protein 4 (HE4) levels correlate with the severity of cystic fibrosis (CF) lung disease. However, there are no data on how HE4 levels alter in patients receiving CFTR modulating therapy.

METHODS

In this retrospective clinical study, 3 independent CF patient cohorts (US-American: 29, Australian: 12 and Irish: 19 cases) were enrolled carrying at least one Class III CFTR CF-causing mutation (p.Gly551Asp) and being treated with CFTR potentiator ivacaftor. Plasma HE4 was measured by immunoassay before treatment (baseline) and 1-6 months after commencement of ivacaftor, and were correlated with FEV₁ (% predicted), sweat chloride, C-reactive protein (CRP) and body mass index (BMI).

RESULTS

After 1 month of therapy, HE4 levels were significantly lower than at baseline and remained decreased up to 6 months. A significant inverse correlation between absolute and delta values of HE4 and FEV₁ (r = -0.5376; P < .001 and r = -0.3285; P < .001), was retrospectively observed in pooled groups, including an independent association of HE4 with FEV₁ by multiple regression analysis (β = -0.57, P = .019). Substantial area under the receiver operating characteristic curve (ROC-AUC) value was determined for HE4 when 7% mean change of FEV₁ (0.722 [95% CI 0.581-0.863]; P = .029) were used as classifier, especially in the first 2 months of treatment (0.806 [95% CI 0.665-0.947]; P < .001).

CONCLUSIONS

This study shows that plasma HE4 levels inversely correlate with lung function improvement in CF patients receiving ivacaftor. Overall, this potential biomarker may be of value for routine clinical and laboratory follow-up of CFTR modulating therapy.

Monogenic Forms of Diabetes Mellitus

In addition to the common types of diabetes mellitus, two major monogenic diabetes forms exist. Maturity-onset diabetes of the young (MODY) represents a heterogenous group of monogenic, autosomal dominant diseases. MODY accounts for 1-2% of all diabetes cases, and it is not just underdiagnosed but often misdiagnosed to type 1 or type 2 diabetes. More than a dozen MODY genes have been identified to date, and their molecular classification is of great importance in the correct treatment decision and in the judgment of the prognosis. The most prevalent subtypes are HNF1A, GCK, and HNF4A. Genetic testing for MODY has changed recently due to the technological advancements, as contrary to the sequential testing performed in the past, nowadays all MODY genes can be tested simultaneously by next-generation sequencing. The other major group of monogenic diabetes is neonatal diabetes mellitus which can be transient or permanent, and often the diabetes is a part of a syndrome. It is a severe monogenic disease appearing in the first 6 months of life. The hyperglycemia usually requires insulin. There are two forms, permanent neonatal diabetes mellitus (PNDM) and transient neonatal diabetes mellitus (TNDM). In TNDM, the diabetes usually reverts within several months but might relapse later in life. The incidence of NDM is 1:100,000-1:400,000 live births, and PNDM accounts for half of the cases. Most commonly, neonatal diabetes is caused by mutations in KCNJ11 and ABCC8 genes encoding the ATP-dependent potassium channel of the β cell. Neonatal diabetes has experienced a quick and successful transition into the clinical practice since the discovery of the molecular background. In case of both genetic diabetes groups, recent guidelines recommend genetic testing.

Subcellular localization of sterol biosynthesis enzymes

Cholesterol synthesis is a complex, coordinated process involving a series of enzymes. As of today, our understanding of subcellular localization of cholesterol biosynthesis enzymes is far from complete. Considering the complexity and intricacies of this pathway and the importance of functions of DHCR7, DHCR24 and EBP enzymes for human health, we undertook a study to determine their subcellular localization and co-localization. Using expression constructs and antibody staining in cell cultures and transgenic mice, we found that all three enzymes are expressed in ER and nuclear envelope. However, their co-localization was considerably different across the cellular compartments. Furthermore, we observed that in the absence of DHCR7 protein, DHCR24 shows a compensatory upregulation in a Dhcr7^-/- transgenic mouse model. The overall findings suggest that the sterol biosynthesis enzymes might not always work in a same functional complex, but that they potentially have different, multifunctional roles that go beyond the sterol biosynthesis pathway. Furthermore, the newly uncovered compensatory mechanism between DHCR7 and DHCR24 could be of importance for designing medications that would improve cholesterol production in patients with desmosterolosis and Smith-Lemli-Opitz syndrome.

Comprehensive genetic testing in children with a clinical diagnosis of ARPKD identifies phenocopies

BACKGROUND

Autosomal recessive polycystic kidney disease (ARPKD) is genetically one of the least heterogeneous ciliopathies, resulting primarily from mutations of PKHD1. Nevertheless, 13-20% of patients diagnosed with ARPKD are found not to carry PKHD1 mutations by sequencing. Here, we assess whether PKHD1 copy number variations or second locus mutations explain these cases.

METHODS

Thirty-six unrelated patients with the clinical diagnosis of ARPKD were screened for PKHD1 point mutations and copy number variations. Patients without biallelic mutations were re-evaluated and screened for second locus mutations targeted by the phenotype, followed, if negative, by clinical exome sequencing.

RESULTS

Twenty-eight patients (78%) carried PKHD1 point mutations, three of whom on only one allele. Two of the three patients harbored in trans either a duplication of exons 33-35 or a large deletion involving exons 1-55. All eight patients without PKHD1 mutations (22%) harbored mutations in other genes (PKD1 (n = 2), HNF1B (n = 3), NPHP1, TMEM67, PKD1/TSC2). Perinatal respiratory failure, a kidney length > +4SD and early-onset hypertension increase the likelihood of PKHD1-associated ARPKD. A patient compound heterozygous for a second and a last exon truncating PKHD1 mutation (p.Gly4013Alafs*25) presented with a moderate phenotype, indicating that fibrocystin is partially functional in the absence of its C-terminal 62 amino acids.

CONCLUSIONS

We found all ARPKD cases without PKHD1 point mutations to be phenocopies, and none to be explained by biallelic PKHD1 copy number variations. Screening for copy number variations is recommended in patients with a heterozygous point mutation.

Interfering effect of maternal cell contamination on invasive prenatal molecular genetic testing

OBJECTIVE

Fetal samples obtained by invasive techniques are prone to maternal cell contamination (MCC), which may lead to false genotyping results. Our aim was to determine 3 molecular genetic tests' sensitivity to MCC.

METHOD

By mixing experiments, 1%, 5%, 10%, 20%, 30%, and 40% MCC was simulated, and significant MCC levels were determined for Sanger DNA sequencing, multiplex ligation-dependent probe amplification (MLPA), and pyrosequencing, a next-generation sequencing method.

RESULTS

For Sanger sequencing, the limit of sensitivity to MCC was 5% to 30%. For MLPA, a higher proportion of MCC (≥40%) was shown to lead to diagnostic uncertainty. In contrast, pyrosequencing proved to be very sensitive to MCC, detecting a proportion as low as 1%.

CONCLUSION

In the case of Sanger sequencing, sensitivity to MCC was variable, while for MLPA, only high levels of MCC proved to be significant. Although the next-generation sequencing method was sensitive to low-level MCC, if MCC level is determined in parallel, accurate quantification of allelic ratios can help to interpret the diagnostic results. Knowledge of significant MCC levels allows correct prenatal diagnosis even if samples are not purely of fetal origin and repeated sampling can be avoided in many of the cases.

Relative anterior microphthalmos in oculodentodigital dysplasia

Here, we report a patient with oculodentodigital dysplasia (ODDD) caused by the c. 413G>A, p.Gly138Asp mutation in the gap junction protein alpha-1 gene. The patient suffered from characteristic dysmorphic features of ODDD. Ophthalmological investigation disclosed microcornea and a shallow anterior chamber, as expected. Surprisingly, the patient had a normal axial length and moderate myopia on both eyes. To the best of our knowledge, this is the first report on ODDD associated with relative anterior microphthalmos and myopia.

Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Background

Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.

Results

In the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 – 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.

Conclusions

Our results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4544-x) contains supplementary material, which is available to authorized users.

Examination of Y-Chromosomal Microdeletions and Partial Microdeletions in Idiopathic Infertility in East Hungarian Patients

Purpose

The aim of this study was to establish the Y chromosome microdeletion and partial AZFc microdeletion/duplication frequency firstly in East Hungarian population and to gain information about the molecular mechanism of the heterogeneous phenotype identified in males bearing partial AZFc deletions and duplications.

Materials and Methods

Exactly determined sequences of azoospermia factor (AZF) region were amplified. Lack of amplification was detected for deletion. To determine the copy number of DAZ and CDY1 genes, we performed a quantitative analysis. The primers flank an insertion/deletion difference, which permitted the polymerase chain reaction products to be separated by polyacrylamide gel electrophoresis.

Statistical Analysis Used

Mann-Whitney/Wilcoxon two-sample test, Kruskal-Wallis test, and two-sample t-probe were used for statistical analysis.

Results

AZFbc deletion was detected only in the azoospermic cases; AZFc deletion occurred significantly more frequently among azoospermic patients, than among oligozoospermic males. The frequency of gr/gr deletions was significantly higher in the oligozoospermic patients than in the normospermic group. The b2/b3 deletion and partial duplications were not different among our groups, while b1/b3 deletion was found only in the azoospermic group. In infertile males and in normozoospermic controls, similar Y haplogroup distribution was detected with the highest frequency of haplogroup P. The gr/gr deletion with P haplogroup was more frequent in the oligozoospermic group than in the normozoospermic males. The b2/b3 deletion with E haplogroup was the most frequent, found only in the normozoospermic group.

Conclusions

Y microdeletion screening has prognostic value and can affect the clinical therapy. In case of Y chromosome molecular genetic aberrations, genetic counseling makes sense also for other males in the family because these types of aberrations are transmittable (from father to son 100% transmission).

A novel homozygous mutation (1619delC) in GPIIb gene associated with Glanzmann thrombasthenia, the decay of GPIIb-mRNA and the synthesis of a truncated GPIIb unable to form complex with GPIIIa

The absence of agonist-induced platelet aggregation and the lack of fibrinogen receptor (GPIIb/IIIa) on the platelet surface demonstrated that the severe hemorrhagic complications of a child of Romany descent were caused by Glanzmann thrombasthenia. DNA sequencing revealed a novel homozygous deletion of a cytosine (1619delC) in the GPIIb gene causing a frameshift and predicting a novel stop codon at position 533 following 24 altered amino acids. Both parents possessed the same deletion in heterozygous form. The amount of GPIIb mRNA in the patient’s platelets was 0.06% of the amount measured in control platelets. Neither GPIIb nor its truncated form could be detected in the platelets of the patient by Western blotting, while a small amount of GPIIIa was demonstrated. Quantitative flow cytometric analysis showed an elevated number of vitronectin receptors, a component of which is GPIIIa, on the patient’s platelets. The surface expression of vitronectin receptor on thrombasthenic, but not on normal platelets was further increased by activation with thrombin receptor agonist peptide. BHK cells transfected with wild type GPIIIa and mutated GPIIb failed to express any mature GPIIb or pro-GPIIb. Immunoprecipitation with a polyclonal antibody recognizing both GPIIb and GPIIIa recovered a 60 kDa truncated form of GPIIb. This band was absent when immunoprecipitation was carried out with an antibody recognizing GPIIIa, suggesting that the truncated protein, lacking calf-1, calf-2 domains and major part of the thigh domain, is unable to form complex with GPIIIa.

Effect of Val34Leu Polymorphism on the Activation of the Coagulation Factor XIII-A

Coagulation factor XIII (FXIII) is a protransglutaminase involved in the last step of the coagulation cascade by stabilising the fibrin clot. Recently, a common variation (FXIII Val34Leu) has been associated with a decreased risk of myocardial infarction and deep venous thrombosis. Val34Leu is critically located near the thrombin activation site of FXIII-A. In this study we investigated its effects on the activation of FXIII. Both recombinant and platelet-derived FXIII Val34Leu variants were shown to be more susceptible to thrombin cleavage than the wild type FXIII. The rate of enzymatic activation of FXIII Val34Leu was found increased, however, the specific activity of fully activated wild type FXIII and the Val34Leu mutant did not differ. During the course of thrombin-induced activation of FXIII fibrin γ-chain dimerisation and α-chain polymerisation developed more rapidly with the Val34Leu mutant. The increased rate of fibrin stabilisation brought about by the Val34Leu FXIII seems to be paradoxically associated with a protective effect against pathological thrombosis.

Abbreviations: AP, activation peptide of factor XIII; FXIII, blood coagulation factor XIII; FXIII-A, factor XIII subunit A; FXIII-A’, proteolytically activated subunit A; FXIII-B, factor XIII subunit B; SDS PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis

Investigation of Thr715Pro P-selectin gene polymorphism and soluble P-selectin levels in type 2 diabetes mellitus

Increased levels of soluble P-selectin (sP-selectin) have been shown in a number of different disorders, e.g. diabetes mellitus (DM) and cardiovascular disease (CVD). Several studies have attempted to demonstrate the association of the most intensively examined variant of P-selectin gene polymorphism (Thr715Pro) with sP-selectin levels in healthy subjects and in CVD, but contradictory data have been reported.To clarify the effect of Pro715 allele on the sP-selectin levels in type 2 DM, we analysed this polymorphism in diabetic patients and compared these data with sP-selectin levels. Type 2 DM patients (n=119), 48 BMImatched non diabetic individuals – consisting mostly of overweight subjects – and 57 healthy volunteers were included in the study.TheThr715Pro polymorphism was analysed by PCR-RFLP, while sP-selectin levels were measured by ELISA. Significantly elevated sP-selectin levels were found in both DM and in overweight subjects compared to healthy controls. We confirmed previous reports that in healthy Pro715 allele carriers lower sP-selectin levels could be measured; however, this difference was only significant in case of lean subjects. No significant difference was detected in sP-selectin level among DM and overweight individuals according to this genotype. However, significant difference was observed in sP-selectin levels in older DM patients compared to younger ones,but these levels were not accounted for by the Thr715Pro polymorphism.We suggest that in type 2 DM individuals, the significantly elevated sP-selectin levels are not due to the Thr715Pro P-selectin gene polymorphism.

Myopia and Late-Onset Progressive Cone Dystrophy Associate to LVAVA/MVAVA Exon 3 Interchange Haplotypes of Opsin Genes on Chromosome X

Purpose

Rare interchange haplotypes in exon 3 of the OPN1LW and OPN1MW opsin genes cause X-linked myopia, color vision defect, and cone dysfunction. The severity of the disease varies on a broad scale from nonsyndromic high myopia to blue cone monochromatism. Here, we describe a new genotype-phenotype correlation attributed to rare exon 3 interchange haplotypes simultaneously present in the long- and middle-wavelength sensitive opsin genes (L- and M-opsin genes).

Methods

A multigenerational family with X-linked high myopia and cone dystrophy was investigated.

Results

Affected male patients had infantile onset myopia with normal visual acuity and color vision until their forties. Visual acuity decreased thereafter, along with the development of severe protan and deutan color vision defects. A mild decrease in electroretinography response of cone photoreceptors was detected in childhood, which further deteriorated in middle-aged patients. Rods were also affected, however, to a lesser extent than cones. Clinical exome sequencing identified the LVAVA and MVAVA toxic haplotypes in the OPN1LW and OPN1MW opsin genes, respectively.

Conclusion

Here, we show that LVAVA haplotype of the OPN1LW gene and MVAVA haplotype of the OPN1MW gene cause apparently nonsyndromic high myopia in young patients but lead to progressive cone-rod dystrophy with deuteranopia and protanopia in middle-aged patients corresponding to a previously unknown disease course. To the best of our knowledge, this is the first report on the joint effect of these toxic haplotypes in the two opsin genes on chromosome X.

Congenital Hyperinsulinism Caused by a De Novo Mutation in the ABCC8 Gene - A Case Report

Congenital hyperinsulinism (CHI) is a rare genetic disorder characterized by inappropriate insulin secretion and severe hypoglycaemia. There are two histological subtypes: diffuse and focal form. Diffuse form is most common in autosomal recessive mutations in ABCC8/KCNJ11 gene, while focal CHI is caused a paternally inherited mutation and a somatic maternal allele loss. Here we report a case of a term male infant presented with severe hyperinsulinaemic hypoglycaemia. Gene panel testing was performed to give rapid genetic diagnosis. We detected the c.4415-13G>A heterozygous mutation in the ABCC8 gene. Targeted genetic testing of the parents proved the de novo origin of the mutation. The mutation has been previously described. The infant received octreotide treatment and is prepared for 18-fluoro-dopa PET-CT examination in order to localize the lesion. Rapid genetic testing might be crucial in the clinical management strategy, with decision algorithms taking into account of the genetic status of the patient.