Muhsin Özdemir

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.

IDH1 mutations is prognostic marker for primary glioblastoma multiforme but MGMT hypermethylation is not prognostic for primary glioblastoma multiforme

PURPOSEnTo establish the frequency of IDH1 mutations and MGMT methylation in primary glioblastomas.nnnEXPERIMENTAL DESIGNnWe screened primary glioblastoma multiforme (GBM) in a population-based study for IDH1 mutations and MGMT methylation and correlated them with clinical data.nnnRESULTSnIDH1 mutations were detected in 5 of 40 primary glioblastomas (12,5%). Primary GBM patients carrying IDH1 mutations were significantly younger, mean age of 41±5.06years, than patients with wild-type IDH1, mean age of 57±2,29years, p=0.011. The mean survival time of all GBM patients with and without IDH1 mutations was 19months (5 cases) and 16months (35 cases), respectively (p>0,05). MGMT methylation was detected in 13 of the 40 patients (32,5%). MGMT-promoter methylation did not correlate with overall survival (OS; p>0,05).nnnCONCLUSIONnIn summary, our study is the first study to investigate the IDH1 mutation status and MGMT methylation in primary GBMs in Turkish population and confirmed IDH1 mutation as a genetic marker for also primary GBMs. Our data are still insufficient for definite ascertainment; and our preliminary results suggest: IDH1 status shows an association with younger age and there is a lack of association between IDH1 mutation and survival time. Furthermore MGMT promoter methylation had no prognostic value and lower frequency in primary glioblastomas.

Prognostic impact of chromosome alterations detected by FISH in Turkish patients with B-cell chronic lymphocytic leukemia

The goal of this study was to evaluate the relation of chromosomal abnormalities detected by fluorescence in situ hybridization (FISH) in the prognosis of B-cell chronic lymphocytic leukemia (B-CLL) patients. We evaluated the common recurrent chromosomal aberrations in 79 B-CLL patients (51 men, 28 women; mean age 64.3+/-1.2) by FISH analysis using 11q22.3 (ATM), 13q14.3 (13S319 and 13S25), CEP12, and 17p13.1 (TP53) specific probes. Of the 79 patients analyzed by FISH, 40 or 50.6% had at least one aberration. In particular, 34 (43%) patients had a single abnormality and 6 (7.6%) patients had 2 abnormalities. The most frequent abnormality was 13q14.3 deletion, which was detected in 26 (32.9%) patients. Trisomy 12 was seen in 12 (15.2%) cases, and was followed by 17p13.1 (TP53) deletions and 11q22.3 (ATM) deletions in 6 (7.6%) and 4 (5.1%) patients, respectively. When the overall frequencies of these chromosomal aberrations were distributed according to RAI stages, the majority of patients with 13q14.3 deletion (55%), trisomy 12 (70%), and ATM or TP53 deletions (66.7 %) were in advanced stages of disease (RAI II-IV). The overall survival durations in good, intermediate, and poor prognostic groups were 51+/-1.3, 50.9+/-8.6, and 12+/-3.3 months, respectively. Our data suggests that FISH analysis of B-CLL patients provides important diagnostic, clinical, and prognostic information which may help clinicians assess the prognosis and make appropriate treatment decisions.

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.

The effects of a heterochromatin polymorphism in chromosome 6 on premature ovarian failure

Abstract Through cytogenetic analysis, heteromorphisms were detected in chromosomes 1,9,16 and Y and defined as non-phenotypic variations. The polymorphism in the centromeric heterochromatin region of chromosome 6 is a rare variant, and only five cases have been documented in the literature. In our study, we used cytogenetic and molecular techniques to detect an increase in the centromeric heterochromatin region in the short arm of both copies of homologous chromosome 6 in a premature ovarian failure (POF) case. The report of this case is important for determining the relationship between fertility and the frequency of rare variants of the centromeric heterochromatin region of chromosome 6 in the general population.