Huseyin Aslan

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.

Rare Variants in the Notch Signaling Pathway Describe a Novel Type of Autosomal Recessive Klippel-Feil Syndrome

Klippel–Feil syndrome is a rare disorder represented by a subgroup of segmentation defects of the vertebrae and characterized by fusion of the cervical vertebrae, low posterior hairline, and short neck with limited motion. Both autosomal dominant and recessive inheritance patterns were reported in families with Klippel–Feil. Mutated genes for both dominant (GDF6 and GDF3) and recessive (MEOX1) forms of Klippel–Feil syndrome have been shown to be involved in somite development via transcription regulation and signaling pathways. Heterotaxy arises from defects in proteins that function in the development of left–right asymmetry of the developing embryo. We describe a consanguineous family with a male proband who presents with classical Klippel–Feil syndrome together with heterotaxy (situs inversus totalis). The present patient also had Sprengels deformity, deformity of the sternum, and a solitary kidney. Using exome sequencing, we identified a homozygous frameshift mutation (c.299delT; p.L100fs) in RIPPLY2, a gene shown to play a crucial role in somitogenesis and participate in the Notch signaling pathway via negatively regulating Tbx6. Our data confirm RIPPLY2 as a novel gene for autosomal recessive Klippel–Feil syndrome, and in addition—from a mechanistic standpoint—suggest the possibility that mutations in RIPPLY2 could also lead to heterotaxy.

NONSENSE β-THALASSEMIA MUTATION AT CODON 37 (TGG>TGA), DETECTED FOR THE FIRST TIME IN THREE TURKISH CASES

Thalassemias are genetically heterogeneous group of disorders with reduced or absent production of globin. β-Thalassemia major can be caused by homozygosity or compound heterozygosity for β-globin gene mutation. Here we report, for the first time in Turkey, three cases who carry the nonsense β-thalassemia (β-thal) mutation at codon 37 (TGG>TGA; Trp→Stop) causing premature stop codon.

Detection of deletions and/or amplifications of genes related with lung cancer by multiplex ligation-dependent probe amplification (MLPA) technique.

Lung cancer has the leading mortality rate among all cancers and it is the second most common cause of death following deaths from cardiovascular diseases. Although it is generally accepted that the tobacco smoke causes lung cancer, not everyone who smokes develops lung cancer. Epidemiologic studies have shown that smokers are 14 times more likely to develop lung cancer than nonsmokers, but only about 11% of heavy smokers develop lung cancer in their lifetime. As a result, some have suggested that genetic factors may predispose people to lung cancer development.

The Prevalence of Gap Junction Protein Beta 2 (GJB2) Mutations in Non Syndromic Sensorineural Hearing Loss in Cukurova Region.

OBJECTIVE To date, studies in all populations showed that mutations in the gene of Gap junction protein beta 2 (GJB2) play an important role in non-syndromic autosomal recessive congenital hearing loss. The aim of this study was to evaluate GJB2 gene of patients with hearing loss in our region using deoxyribonucleic acid (DNA) sequencing method and to demonstrate region-specific mutation and polymorphism distribution. MATERIALS AND METHODS Patients who had bilateral severe sensorineural non-syndromic hearing loss identified by audiologic evaluation were included. Peripheral blood samples were collected and the GJB2 gene exon1 and exon 2 regions were amplified by polymerase chain reaction (PCR). Obtained PCR products were sequenced by the DNA sequence analysis method (SeqFinder Sequencing System; ABI 3130; Foster City, CA, USA) and analyzed using the SeqScape software. RESULTS Of the 77 patients, 16 had homozygous or heterozygous mutation. CONCLUSION The mutation of 35delG, which is known as the most frequent mutation of GJB2 gene, was also the most frequently seen mutation at a ratio of 5.5% in patients with hearing loss in our region; this was followed by the V27I mutation. As this is the first study conducted by sequence analysis in our region, it was worth to be presented in terms of showing the distribution of mutation.

Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1–D2 region sufficient for identification of clinical fungi?

Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour‐intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1–D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1–D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.

Hypomyelination and congenital cataract: Identification of novel mutations in two unrelated families

BACKGROUND Hypomyelination and congenital cataract (HCC) is a rare autosomal recessive white matter disorder characterized by congenital cataract, progressive neurologic impairment, and myelin deficiency in the central and peripheral nervous system, caused by mutations in the FAM126A gene. AIMS To report three patients of two unrelated families segregating novel mutations. METHODS clinical, neurophysiological, neuroradiologic and molecular investigations were carried out. RESULTS All patients show bilateral congenital cataract and progressive neurological impairment with peripheral neuropathy. The clinical phenotype is consistent with the severe form of HCC. Brain magnetic resonance imaging show the combination of a diffuse hypomyelination with superimposed periventricular white matter signal abnormalities. CONCLUSIONS this study describes three additional HCC patients indicating that this recently defined leukoencephalopathy should be included in the differential diagnosis of hypomyelination in childhood. The peculiar clinical and neuroradiologic findings are useful to properly address molecular investigations and allow the differential diagnosis between HCC and other hypomyelinating forms.

Plasminogen activator inhibitor-1 5G/5G genotype is associated with early spontaneous recanalization of the infarct-related artery in patients presenting with acute ST-elevation myocardial infarction.

BackgroundWe aimed to examine the association between plasminogen activator inhibitor-1 (PAI-1) genetic polymorphism and early spontaneous recanalization in patients presenting with acute ST-elevation myocardial infarction. MethodsPatients admitted to our emergency department with ST-elevation myocardial infarction in the first 6 h of symptom onset were included. An immediate primary percutaneous coronary intervention was performed. Patients were grouped according to the initial patency of the infarct-related artery (IRA) as follows: total occlusion (TO) group [Thrombolysis in Myocardial Infarction (TIMI) 0–1 flow in the IRA], partial recanalization group (TIMI 2 flow in the IRA), and complete recanalization (CR) group (TIMI 3 flow in the IRA). PAI-1 4G/5G polymorphism was detected using the real-time PCR method. ResultsThere were 107 patients in the TO group, 30 patients in the partial recanalization group, and 45 patients in the CR group. When we evaluated degrees of patency according to the PAI-1 genotype, TO of the IRA was the highest in patients with the PAI 4G/4G genotype (PAI-1 4G/4G: 66.7%, PAI-1 4G/5G: 65.9%, PAI-1 5G/5G: 40.4%) and CR of the IRA was the highest in patients with the PAI 5G/5G genotype (PAI-1 5G/5G: 38.5%, PAI-1 4G/5G: 19.8%, PAI-1 4G/4G: 17.9%). The distribution of genotypes in different degrees of patency of IRA was statistically significant (P=0.029). In logistic regression analysis, the PAI-1 5G/5G genotype was associated independently with the spontaneous CR of the IRA (odds ratio: 2.875, 95% confidence interval [1.059–7.086], P=0.038). ConclusionPatients with the PAI-1 5G/5G genotype seem to be luckier than others in terms of early spontaneous recanalization of the IRA. Further prospective studies with large patient populations are required for more precise results.

The first report of a patient with probable variant creutzfeldt-jakob disease in Turkey.

Variant Creutzfeldt-Jakob disease (vCJD) was first reported in the UK in 1996. Here, we report the first Turkish case of vCJD. A 47-year-old man, who has never lived outside of Turkey and had had no transfusion, was admitted to the University Hospital with speech disorder, cognitive decline and ataxia following depression, irritability, and personality change. The immunoassay of the 14-3-3 protein in the cerebrospinal fluid was negative. Brain magnetic resonance imaging revealed high-signal lesions involving the bilateral caudate and lentiform nucleus on T2- and diffusion-weighted imaging. The patient developed akinetic mutism 10 months after disease onset. The clinical presentation and neuroimaging findings were compatible with the vCJD cases reported since 1996 and met the World Health Organization’s case definition for probable vCJD.

Acrodermatitis enteropathica: A novel mutation of the SLC39A4 gene in a Turkish boy.

pustules on the trunk with a wedge-shaped symmetrical distribution (Fig. 1a–d). Punch biopsy from the lesion showed subcorneal spongiotic pustules composed of neutrophils with a negative result on Gram staining. The basal layer presented vacuolar degeneration, and superficial perivascular inflammatory infiltrations composed of lymphocytes and eosinophils were evident in the dermis (Fig. 1e,f). Laboratory examinations showed normal results. She had been given systemic and topical steroid over 3 weeks with poor response. Doxycycline 200 mg/day was started and the lesions resolved in 2 weeks leaving a brown reticulated hyperpigmentation. Based on the clinical findings, the skin biopsy result and dramatic response to doxycycline, the patient was diagnosed with pustular prurigo pigmentosa (PP). Prurigo pigmentosa is characterized by the sudden onset of pruritic erythematous papules, involving the trunk and neck that coalesce to reticulated and mottled patches. In severe cases, they may form edematous infiltrative plaques, and the vesicles are rarely found. Lesions resolve within several weeks leaving postinflammatory hyperpigmentations, and recurrences are usual. Because the pustular type of PP has not been reported, we considered various pustular diseases first, including subcorneal pustular dermatosis, acute generalized exanthematous pustulosis and pustular psoriasis. The treatment and prognosis of PP differ with these diseases, therefore, early diagnosis with proper treatment would be important. The exact cause and pathogenesis of PP are unclear. Even the histology of PP is non-specific. B€ oer et al. emphasized the presence of neutrophils in the histopathological findings. From the histological finding of this case, which showed nonfollicular subcorneal sterile spongiotic neutrophilic pustulosis, we could support the importance of neutrophilic finding of PP, and hypothesize that the pustules had formed as a result of severe spongiosis and liquefaction of the basal cell layer. A variety of agents are used in the treatment of PP, the most effective of which are oral antibiotics such as minocycline, doxycycline and sulfonamides. Medications that have been reported to be useful in PP are due to their ability to inhibit the migration or function of neutrophils. This case showed a dramatic response to doxycycline with the inhibition of new pustule formation in 2 weeks. Finally, the patient was diagnosed with pustular PP, because of clinical characteristics showing sudden onset of symmetrical pruritic skin lesions, histopathological findings, and clinical course resolving with doxycycline and leaving postinflammatory reticulated hyperpigmentations. In summary, PP can present with pustular lesions and thus should be considered in the differential diagnosis of pruritic pustular diseases. Clinical features which include the distribution of lesions, coexistence of reticulate pigmentation, and good response to minocycline or doxycycline therapy distinguish PP from other dermatoses.