Oguz Cilingir

Investigation of key miRNAs and target genes in bladder cancer using miRNA profiling and bioinformatic tools

Despite the association of several miRNAs with bladder cancer, little is known about the miRNAs’ regulatory networks. In this study, we aimed to construct potential networks of bladder-cancer-related miRNAs and their known target genes using miRNA expression profiling and bioinformatics tools and to investigate potential key molecules that might play roles in bladder cancer regulatory networks. Global miRNA expression profiles were obtained using microarray followed by RT-qPCR validation using two randomly selected miRNAs. Known targets of deregulated miRNAs were utilized using DIANA-TarBase database v6.0. The incorporation of deregulated miRNAs and target genes into KEGG pathways were utilized using DIANA-mirPath software. To construct potential miRNA regulatory networks, the overlapping parts of three selected KEGG pathways were visualized by Cytoscape software. We finally gained 19 deregulated miRNAs, including 5 ups- and 14 down regulated in 27 bladder-cancer tissue samples and 8 normal urothelial tissue samples. The enrichment results of deregulated miRNAs and known target genes showed that most pathways were related to cancer or cell signaling pathways. We determined the hub CDK6, BCL2, E2F3, PTEN, MYC, RB, and ERBB3 target genes and hub hsa-let-7c, hsa-miR-195-5p, hsa-miR-141-3p, hsa-miR-26a-5p, hsa-miR-23b-3p, and hsa-miR-125b-5p miRNAs of the constructed networks. These findings provide new insights into the bladder cancer regulatory networks and give us a hypothesis that hsa-let-7c, hsa-miR-195-5p, and hsa-miR-125b-5p, along with CDK4 and CDK6 genes might exist in the same bladder cancer pathway. Particularly, hub miRNAs and genes might be potential biomarkers for bladder cancer clinics.

Study on potential role of apolipoprotein E in recurrent pregnancy loss

The role of apolipoprotein E (Apo E) gene polymorphisms in the etiology of recurrent pregnancy loss (RPL) is not clearly understood. We evaluated this polymorphism in unexplained pregnancy losses in a group of Turkish women. In our prospective case-control study, 45 well-characterized RPL cases were examined for their Apo E genotypes, based on restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-amplified fragments. The observed genotypes were compared with those obtained from equal number matched controls. We observed similar Apo E genotypes and E2, E3 and E4 allele frequency distribution among RPL patients and controls. The allele frequencies obtained in patients and controls, respectively, were as follows: E2=8 (9%) and 12 (13.4%) (P=0.342), E3=66 (73.3%) and 60 (66.6%) (P=0.328) and E4=16 (17.7%) and 18 (20%) (P=0.703). Our data did not support the association of Apo E gene polymorphisms with RPL as reported by previous studies. We endorse adequate characterization of RPL cases and adequate sample size prior to addressing such studies.

Prevalence of nonclassic congenital adrenal hyperplasia in Turkish children presenting with premature pubarche, hirsutism, or oligomenorrhoea.

Background. Nonclassic congenital adrenal hyperplasia (NCAH), caused by mutations in the gene encoding 21-hydroxylase, is a common autosomal recessive disorder. In the present work, our aim was to determine the prevalence of NCAH presenting as premature pubarche (PP), hirsutism, or polycystic ovarian syndrome (PCOS) and to evaluate the molecular spectrum of CYP21A2 mutations in NCAH patients. Methods. A total of 126 patients (122 females, 4 males) with PP, hirsutism, or PCOS were included in the present study. All patients underwent an ACTH stimulation test. NCAH was considered to be present when the stimulated 17-hydroxyprogesterone plasma level was >10 ng/mL. Results. Seventy-one of the 126 patients (56%) presented with PP, 29 (23%) with PCOS, and 26 (21%) with hirsutism. Six patients (4,7%) were diagnosed with NCAH based on mutational analysis. Four different mutations (Q318X, P30L, V281L, and P453S) were found in six NCAH patients. One patient with NCAH was a compound heterozygote for this mutation, and five were heterozygous. Conclusion. NCAH should be considered as a differential diagnosis in patients presenting with PP, hirsutism, and PCOS, especially in countries in which consanguineous marriages are prevalent.

Exploring the relationship between the severity of oligozoospermia and the frequencies of sperm chromosome aneuploidies.

The study was aimed to investigate the association between the degree of oligozoospermia and sperm chromosome aneuploidy frequencies in male infertility and to determine whether chromosomal profiles of sperm nuclei would be used for a supportive test before additive reproduction technics. The meiotic segregation profiles of chromosomes X, Y, 13, 18 and 21 were compared by fluorescent in‐situ hybridisation (FISH) on the spermatozoa of 30 normally karyotyped oligozoospermic (10 mild, 11 moderate, nine severe) cases without Y‐microdeletions, and 10 normozoospermic cases. The results showed significantly higher frequencies of chromosomes 13, 18, 21 disomies (P < 0.001) in the group of patients with moderate and severe oligozoospermia compared with the disomy frequencies of normozoospermic group. The statistically significant differences were also determined in disomy frequencies of sex chromosomes (XY, XX and YY) in between oligozoospermic and normozoospermic groups (P < 0.001, P < 0.001, P < 0.040, respectively). Because oligozoospermic patients are the ones consulted the most for assisted reproductive techniques, identification of sperm aneuploidy rates in men could be considered as an appropriate supportive test before the reproductive implementations. Furthermore, the patients should be counselled with respect to genetic screening results for the potential risk of aneuploid embryo and pre‐implantation genetic diagnosis or prenatal diagnosis.

Clinical heterogeneity associated with TUBB3 gene mutation in a Turkish family with congenital fibrosis of the extraocular muscles.

Congenital fibrosis of the extraocular muscles (CFEOM) includes rare genetic strabismus syndromes with restriction.1 Four types of CFEOM have been identified; CFEOM1 (1A and B), CFEOM2, CFEOM3 (3A,...

Sequencing of a 306 bp Region of the ANXA11 Gene Containing the rs1049550 Polymorphism for Sarcoidosis Susceptibility in TurkishPatients

Sarcoidosis is a multisystemic immune disorder with unknown etiology. The disease is characterized by the spread of noncaseating epithelioid granulomas. Recent data from Genome Wide Association Studies (GWAS) have identified annexin A11 (ANXA11) as a new sarcoidosis susceptibility gene. These studies further indicated a strong association of a single nucleotide polymorphism (rs1049550) with sarcoidosis. Our aim was to determine whether the rs1049550 is associated with sarcoidosis in Turkish patients and to scan a 306 bp region of ANXA11 for other variations associated with sarcoidosis. Genomic DNA was isolated from the leukocytes of 53 sarcoidosis patients and 52 controls. A 306 bp region of ANXA11 encompassing rs1049550 was amplified by PCR, and the amplicons were sequenced using the Sanger method. The sequence data of both patients and controls were analyzed using the BLAST database to identify variations. The allele and genotype frequencies of the groups were analyzed using the chisquare test. The rs1049550 polymorphism was the only genetic variation observed in the 306 bp region. There was no statistically difference (χ2=2.689, P=0.273) when the frequencies of the CC, CT and TT genotypes in the sarcoidosis group (58.5%, 30.2% and 11.3%, respectively) were compared with the corresponding genotypes in the control group (65.4%, 17.3% and 17.3%, respectively). Furthermore, the allele frequencies for the rs1049550 polymorphism were not significantly different (χ2=0.006, P=0.940) when comparing the sarcoidosis patients (C=73.6%, T=26.4%) with the controls (C=74.0%, T=26.0%). Our results suggest that the ANXA11 rs1049550 polymorphism is not a genetic predisposition marker for Turkish patients with sarcoidosis.

IS THERE A RELATIONSHIP BETWEEN APOE GENOTYPES AND HOSPITALIZATION OF DEMENTIA PATIENTS

Background: To determine whether observed relationship between the genotype distribution of Apolipoprotein E and number and reason of hospitalisations amongs demented patients. Methods: We collected data on the basis of data from 630 dementia patients admitting to Eskisehir Osmangazi University dementia outpatient clinic who consented to the genotyped until present from 2000.Results: Themost common part of our patients was consisted of Alzheimer disease (41.9%). Remaining part were subsequently vascular dementia (33.3%), Frontotemporal dementia (7.6%), other group (tumors, hydrocephalus, endocrine vs. 5.6%), Mild cognitive impairment (4.4%), Lewy body dementia (3.3%), Corticobasal disorder (2.4%) and Progressive supranuclear palsy (1.4%). APOE genotype frequencies were 0.6 percent for E2/E2, 0.8 percent for E2/E4, 5.1 percent for E4/E4, 9 percent for E2/E3, 21.7 percent for E3/E4, 62.7 percent for E3/E3. While, In Alzheimer dementia was seen more often E3/3, 3/4, 4/4 than other dementia, the frequency E3/3, 2/3 and 3/4 were higher detected in vascular dementia, respectively. In frontotemporale dementia patients were no seen E4/4, 2/4 and 2/2 alleles. Vascular dementia patients admitted the most times to hospital than other dementia (<0.001). In contrast, Alzheimer patients developed the most complication during their disease (<0.05). These complications were respectively urinary tract (48%) or chest infections (36%), trauma (9%), the prerenal azotemia (4%) and deficiency of feeding (3%). Neither admitting to hospital nor complication type and number were no found differences in APOE genotypes. The used drugs like antidepressant or neuroleptics did not effect to depend on extraordinary events in demented patients. The differences between initial and last MiniMental Status Examination in all dementia patients did not observed the relationship the type of dementia and genotypes distribution of APOE. Conclusions: In conclusion, the APOE genotypes, especially APOE3/4 and 4/4, are not a significant predictor of number and reason of hospitalizations and complication except the natural progression of disease. It is not socio demographic data and can be accepted pathological data.

Performance of MLPA as a screening method for aneuploidy in uncultured amniocytes.

OBJECTIVE To test whether the Multiplex Ligation-dependent Probe Amplification (MLPA) technique can be used as a screening test for rapid diagnosis of aneuploidies in uncultured amniocentesis. MATERIAL AND METHODS In this prospective blind study, MLPA with chromosomes 13,18,21,X and Y specific probe mixes was performed in 500 amniotic fluid samples. Chromosome copy numbers were determined by analyzing size and peak area for each MLPA probe. Results were compared with those of karyotyping/FISH. RESULTS Conclusive test results were obtained in 98% of the samples, whereas 10 were inconclusive. In all conclusive tests, the MLPA results were concordant with that of cytogenetic and/or FISH analyses. There were no false-positive results. A case with 69,XXX triploidy could not be diagnosed by MLPA. In total, 28 aneuploidies were diagnosed. There were no false-positive results. The performance of each probe was determined. CONCLUSION MLPA is a rapid, simple and reliable assay for aneuploidy screening in uncultured amniocytes.