Introducing exome sequencing as part of the diagnostic algorithm for pediatric nephrology patients in Bulgaria - a single-center experience.

INTRODUCTION: In pediatric kidney patients, where clinical presentation is often not fully developed and renal biopsy too risky or inconclusive, it may be difficult to establish the underlying pathology. In cases such as these, genetic diagnosis may be used to guide the treatment, prognosis and counselling. Given the large number of genes involved in kidney disease, introducing next generation sequencing with extended gene panels as part of the diagnostic algorithm presents a viable solution. METHODS: A cohort of 87 consecutive independent cases (83 children and 4 terminated pregnancies) with renal disease were recruited. Exome sequencing with MiSeq or NovaSeq 6 000 (Illumina) platforms and analysis of extended gene panels was used for genetic testing. RESULTS: Depending on the presenting pathology, the cases were grouped as patients with glomerular disease, ciliopathies, congenital anomalies, renal electrolyte imbalances and chronic/acute kidney disease. The overall diagnostic yield was app. 42% (37 out of 87) with most disease-causing mutations found in COL4A3, COL4A4, COL4A5 and PKHD1 genes. A change or clarification of preliminary diagnosis, or adjustment of initial treatment plan based on the results from the genetic testing was made for app. one third of the children with meaningful genetic findings (11 out 37). DISCUSSION: Our results prove the value of targeted exome sequencing as non-invasive, versatile and reliable diagnostic tool for pediatric renal disease patients. Providing genetic diagnosis will help for better understanding of disease etiology and will give basis for optimal clinical management and insightful genetic counseling.

Serum miR-21 and miR-29a expression in systemic sclerosis patients.

OBJECTIVES: The aim of our study was to evaluate the expression levels of miR-21 and miR-29a in the serum of systemic sclerosis (SSc) patients and to determine their correlation with clinical and immunological parameters. METHODS: 34 patients fulfilling the ACR/EULAR 2013 classification criteria for SSc were included in the study. miR-21 and miR-29a expression levels in the serum were determined by PCR (SYBR Green technology). 2-ΔΔCt method was used for analysis. 14 healthy donors were used as controls (HCs). RESULTS: Expression levels of miR-21 were upregulated in the serum of 17 (50.0%) of the patients. The expression of miR-29a was downregulated in 15 (44.12%) of the SSc patients. Receiver operating characteristic (ROC) curve analysis was conducted in order to evaluate the diagnostic accuracy of the expression levels of the studied miRNAs in the serum. Area under the curve (AUC) for miR-21 was 0.634 (95% CI=0.479-0.790), p=0.147 with 64.7% sensitivity and 64.3% specificity. AUC for miR-29a was 0.605 (95% CI=0.420-0.790), with 64.3% sensitivity and 52.9% specificity but without statistical significance (p=0.257). The multimarker analysis of the ROC curves for both miRNAs showed AUC=0.714 (95% CI=0.569-0.860), p=0.021 with 79.4% sensitivity and 42.9% specificity. Levels of miR-29a correlated with the levels of miR-21 in the serum (with Spearman correlation coefficient 0.517, p=0.00017) and with the presence of anti-Scl70 antibodies in the serum (with Spearman correlation coefficient 0.438, p=0.010). CONCLUSIONS: Our data showed a deregulation of miR-21 and miR-29a in the serum of patients with SSc which could suggests their potential role in the disease pathogenesis. Further analysis with higher number of patients is needed to confirm if these miRNAs could be used in the clinical practice as diagnostic biomarkers as well as biomarkers for both disease activity and progression.

CD3Z polymorphisms and promoter hypermethylation in dermatomyositis - the role of cytosine-phosphate-guanine-related single nucleotide polymorphisms.

BACKGROUND: Decreased expression of the T cell receptor (TCR) ζ-chain has been reported in autoimmune diseases. Recent evidence suggests that this deficiency may be due to polymorphisms in the CD3Z (CD247) gene and/or due to promoter hypermethylation. METHODS: Altogether 131 subjects - 36 with dermatomyositis (DM) and 95 healthy controls were genotyped for rs1052230 G > C and rs1052231 T > A polymorphisms using TaqMan assay. The rs840015 G > A polymorphism was analyzed by direct sequencing. The promoter methylation status was analyzed by Sanger sequencing of bisulfite converted DNA. RESULTS: The rs1052230GC genotype and C allele and the rs1052231TA genotype and T allele were found to correlate with photosensitivity as well as the rs1052230C/rs1052231T haplotype. The rs1052231TA genotype was found to be associated with cutaneous disease. The rs840015GG genotype was found increased among patients with DM, leading to increased OR 2.4. On the contrary, the rs840015GA genotype appeared to be protective for the development of DM. From the 11 cytosine-phosphate-guanine (CpG) islands analyzed, only the 8th island showed a difference in its methylation due to the polymorphism rs840015 G > A within this island, as our results suggest. In this way the presence of AA genotype led to no methylation and the presence of the GG genotype was associated with hemimethylation. CONCLUSION: The CD247 rs1052230 G > C and rs1052231 T > A polymorphisms appeared to have a disease-modifying role. The rs840015GA genotype being associated with reduced methylation has a protective role for the development of dermatomyositis and our results suggest that CpG related single nucleotide polymorphisms may play an important role in autoimmunity.

Whole peripheral blood miR-146a and miR-155 expression levels in Systemic lupus erythematosus patients.

Objective: To evaluate the diagnostic value of peripheral blood microribonucleic acid (miRNA, miR)-146a and miR-155 expression in systemic lupus erythematosus (SLE). Methods: Expression levels of miR-155 and miR-146a in whole peripheral blood samples from 40 SLE patients and 32 healthy controls (HCs) were determined by quantitative reverse transcription-polymerase chain reaction qRT-PCR (SYBR Green technology) and 2-∆∆Ct method was used for analysis. SPSS v20 was used for receiver operating characteristic (ROC) curve and Spearman correlation analysis. Results: Whole peripheral blood expression levels of miR-146a and miR-155 were overexpressed in 62.5% and 50%, respectively, of the SLE patients compared to HCs. The ROC curve analysis showed that the expression levels of miR-146a could discriminate SLE patients from HCs with area under the curve (AUC)=0.711 (95% CI: 0.585÷0.837, p=0.002, with 82.5% sensitivity and 56.2% specificity. The diagnostic accuracy of miR-155 was lower with AUC=0.691 (95% CI: 0.566÷0.817, p=0.005, with 77.5% sensitivity and 50.0% specificity. The diagnostic accuracy did improve when combination of the studied miRNAs was used in multimarker ROC curve analysis (AUC=0.716, 95% CI: 0.590÷0.842, p=0.002, 82.5% sensitivity and 56.2% specificity). miR-146a and miR-155 showed correlation with the diagnosis (rs=0.363 and 0.330, respectively) and the age of the patients (rs =0.239 and 0.366, respectively), and miR-155 showed correlation with the presence of secondary Raynaud syndrome (Spearman correlation coefficient=0.250) Conclusions: Our data showed that the expression levels of miR-146a and miR-155 in PB could be used as diagnostic biomarkers for SLE patients but larger study is needed to confirm these results. Key words: peripheral blood, miRNA, expression, systemic lupus erythematosus, biomarker.

BPIFA1 Gene Expression in the Human Middle Ear Mucosa.

OBJECTIVE: The bactericidal/permeability-increasing, fold-containing family member A1 (BPIFA1) gene codes a secretory protein (BPIFA1), which is present in the respiratory tract mucosa, and is part of the innate immune system. This study aimed to prove that BPIFA1 gene expression exists in the human middle ear mucosa. MATERIALS AND METHODS: In total, 32 patients participated in the study between March 2016 and September 2016. Seventeen patients had chronic otitis media with cholesteatoma (COMC) and 15 had bilateral sensorineural hearing loss (BSHL). The patients with COMC underwent radical mastoidectomy with cholesteatoma removal and those with BSHL underwent cochlear implantation. Part of the processus mastoideus mucosa was examined for BPIFA1 gene expression and the two groups were compared. RESULTS: For the first time, BPIFA1 gene expression was examined in the mucosa of the human middle ear, and it was verified in 100% (n=32) of the participants. We confirmed that there is a difference in the BPIFA1 expression in 83.33% of the patients with COMC compared to the patients with BSHL but this difference was not statistically significant (p=0.947; probably due to the low number of participants in this group). CONCLUSION: It is highly likely that the BPIFA1 protein participates in the non-specific immune defense of the middle ear and is relevant to the pathogenesis of the inflammatory diseases of the middle ear.

Polymorphisms in androgen metabolism genes AR, CYP1B1, CYP19, and SRD5A2and prostate cancer risk and aggressiveness in Bulgarian patients.

BACKGROUND/AIM: The aim of our study was to elucidate the role of polymorphisms in AR, CYP1B1, CYP19, and SRD5A2 genes for prostate cancer (PC) development in Bulgarian patients. MATERIALS AND METHODS: We genotyped 246 PC patients and 261 controls (155 with benign prostate hyperplasia and 107 healthy population controls) using direct sequencing, PCR-RFLP, SSCP, and fragment analysis. RESULTS: The allele and genotype frequencies of most of the studied variants did not differ significantly between cases and controls. Increased frequencies of the C/C genotype and C allele of rs1056837 in CYP1B1, and genotype 7/8 of the (TTTA)n repeat polymorphism in CYP19, were observed in patients in comparison with controls.The 8/9 and the 7/12 genotypes of (TTTA)n in CYP19 showed suggestive evidence for association with decreased prostate cancer risk and the risk for aggressive disease, respectively. The haplotype analysis revealed 2 CYP1B1 haplotypes associated with PC risk reduction. CONCLUSION: Some CYP1B1 haplotypes and genotypes of the CYP19 (TTTA)n repeat appeared to be associated with disease risk or aggressiveness in Bulgarian PC patients. In contrast, the SRD5A2 polymorphisms (V89L and (TA)n repeat), the CAG repeat in AR, and the Arg264Cys variant in CYP19A1 are most likely not implicated in prostate carcinogenesis.

Combinations of serum prostate-specific antigen and plasma expression levels of let-7c, miR-30c, miR-141, and miR-375 as potential better diagnostic biomarkers for prostate cancer.

In the current study, expression levels of let-7c, miR-30c, miR-141, and miR-375 in plasma from 59 prostate cancer (PC) patients with different clinicopathological characteristics and two groups of controls: 16 benign prostatic hyperplasia (BPH) samples and 11 young asymptomatic men (YAM) were analyzed to evaluate their diagnostic and prognostic value in comparison to prostate-specific antigen (PSA). miR-375 was significantly downregulated in 83.5% of patients compared to BPH controls and showed stronger diagnostic accuracy (area under the curve [AUC]=0.809, 95% CI: 0.697-0.922, p=0.00016) compared with PSA (AUC=0.710, 95% CI: 0.559-0.861, p=0.013). Expression levels of let-7c showed potential to distinguish PC patients from BPH controls with AUC=0.757, but the result did not reach significance. Better discriminating performance was observed when combinations of studied biomarkers were used. Sensitivity of 86.8% and specificity of 81.8% were reached when all biomarkers were combined (AUC=0.877) and YAM were used as calibrators. None of the studied microRNAs (miRNAs) showed correlation with clinicopathological characteristics. PSA levels were significantly correlated with the Gleason score, tumor stage, and lymph node metastasis with Spearman correlation coefficients: 0.612, 0.576, and 0.458. In conclusion, the combination of the studied circulating plasma miRNAs and serum PSA has the potential to be used as a noninvasive diagnostic biomarker for PC screening outperforming the PSA testing alone.

Auditory outcome after cochlear implantation in patients with congenital nonsyndromic hearing loss: influence of the GJB2 status.

OBJECTIVE: To compare the audiologic outcome after cochlear implantation between 2 groups of patients with congenital nonsyndromic sensorineural hearing loss. STUDY DESIGN: Retrospective cohort study. SETTING: Department of Otorhinolaryngology, University hospital (tertiary referral center). PATIENTS: From a bigger pool of implanted patients, 2 groups, each numbering 30 were enrolled. The patients from the first group were diagnosed with a Connexin 26 mutation (GJB2), whereas all of the patients from the second cohort were with a wild type genotype. Both groups were age matched, 1 to 7 years old at the age of implantation, with diagnosed congenital nonsyndromic sensorineural hearing loss. MAIN OUTCOME MEASURES: Both groups were evaluated with the help evaluation of auditory responses to speech/EARS/test battery - LiP test (Listening Progress Profile), MTP tests 3,6,12 (Monosyllabic-Trochee-Polysyllabic Test), GASP test (Glendonald Auditory Screening Procedure), and others. Follow-up period was at least 36 months. RESULTS: Mean test scores were compared at the 1st, 6th, 12th, 24th, and 36th month. LiP outcome was significantly better (p < 0.05) for the GJB2-related cohort for the whole follow-up period except at the first month. MTP3, 6, and 12 tests displayed the same statistically significant outcome in favor of the first group. In the open-set test GASP, the difference was apparent: 1.22, 2.40, 5.59, and 7.40 mean scores at the 6th, 12th, 24, and 36th months for the first cohort versus 0.00, 0.07, 0.81, and 1.74 for the GJB2-unrelated patients. CONCLUSION: The results from our study suggest that children with GJB2-related deafness show better auditory performance after cochlear implantation than age-matched children with GJB2-nonrelated sensorineural hearing loss.