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Publication Open Access A novel ICK mutation causes ciliary disruption and lethal endocrine-cerebro-osteodysplasia syndrome(BioMed Central, 2016) Oud, M.M.; Bonnard, C.; Mans, D.A.; Altunoğlu, U.; Tohari, S.; Ng, A.Y.J.; Eskin, A.; Lee, H.; Rupar, C.A.; Wagenaar, N.P.; Wu, K.M.; Lahiry, P.; Pazour, G.J.; Nelson, S.F.; Hegele, R.A.; Roepman, R; Venkatesh, B.; Siu, V.M.; Reversade, B.; Arts, H.H.; N/A; Kayserili, Hülya; Faculty Member; School of Medicine; 7945Background: Endocrine-cerebro-osteodysplasia (ECO) syndrome [MIM:612651] caused by a recessive mutation (p.R272Q) in Intestinal cell kinase (ICK) shows significant clinical overlap with ciliary disorders. Similarities are strongest between ECO syndrome, the Majewski and Mohr-Majewski short-rib thoracic dysplasia (SRTD) with polydactyly syndromes, and hydrolethalus syndrome. In this study, we present a novel homozygous ICK mutation in a fetus with ECO syndrome and compare the effect of this mutation with the previously reported ICK variant on ciliogenesis and cilium morphology. Results: Through homozygosity mapping and whole-exome sequencing, we identified a second variant (c.358G > T; p.G120C) in ICK in a Turkish fetus presenting with ECO syndrome. In vitro studies of wild-type and mutant mRFP-ICK (p.G120C and p.R272Q) revealed that, in contrast to the wild-type protein that localizes along the ciliary axoneme and/or is present in the ciliary base, mutant proteins rather enrich in the ciliary tip. In addition, immunocytochemistry revealed a decreased number of cilia in ICK p.R272Q-affected cells. Conclusions: Through identification of a novel ICK mutation, we confirm that disruption of ICK causes ECO syndrome, which clinically overlaps with the spectrum of ciliopathies. Expression of ICK-mutated proteins result in an abnormal ciliary localization compared to wild-type protein. Primary fibroblasts derived from an individual with ECO syndrome display ciliogenesis defects. In aggregate, our findings are consistent with recent reports that show that ICK regulates ciliary biology in vitro and in mice, confirming that ECO syndrome is a severe ciliopathy.Publication Open Access Al2O3 micro- and nanostructures affect vascular cell response(Royal Society of Chemistry (RSC), 2016) Kiefer, Karin; Akpınar, Gürler; Haidar, Ayman; Ikier, Tuba; Akkan, Çağrı Kaan; Akman, Erhan; Lee, Juseok; Miro, Marina Martinez; Kaçar, Elif; Demir, Arif; Veith, Michael; Kasap, Murat; Kesmez, Mehmet; Abdul-Khaliq, Hashim; Aktaş, Cenk; N/A; Ural, Dilek; Faculty Member; School of Medicine; 1057In-stent restenosis (ISR) is one of the most common and serious complications observed after stent implantation. ISR is characterized by the inordinate proliferation of smooth muscle cells (SMC) that leads to narrowing of the blood vessels. To achieve a healthy endothelium, it is critical to selectively enhance the growth of endothelial cells (EC) while suppressing the growth of smooth muscle cells, which is still a major challenge and yet to be achieved. In this study, novel surfaces have been developed to support the selective growth of endothelial cells. Micro-and nanostructured Al2O3 surfaces with unique topographical features were fabricated and tested. Surface characterization and cellular response of endothelial cells (HUVEC) as well as smooth muscle cells (HUVSMC) has been investigated at cellular and molecular levels. A topography driven selective cell response of ECs over SMCs was demonstrated successfully. This selective response of ECs was also analyzed at protein levels in order to understand the basic mechanism.Publication Open Access Antioxidant SMe1EC2 modulates pentose phosphate pathway and glutathione-dependent enzyme activities in tissues of aged diabetic rats(De Gruyter, 2017) Gök, Müslüm; Sayın Şakul, Arzu Ayşe; Arı, Nuray; Stefek, Milan; Karasu, Çimen; N/A; Ulusu, Nuriye Nuray; Faculty Member; School of Medicine; 6807The pentose phosphate pathway and glutathione-associated metabolism are the main antioxidant cellular defense systems. This study investigated the effects of the powerful antioxidant SMe1EC2 (2-ethoxycarbonyl-8-methoxy-2,3,4,4a,5,9b-hexahydro-1H-pyrido[4,3-b] indolinium dichloride) on pentose phosphate pathway (PPP) and glutathione-dependent enzyme activities in aged diabetic and aged matched control rats. Diabetes was induced by streptozotocin injection in rats aged 13–15 months. Diabetic and control rats were divided into two subgroups, one untreated and one treated with SMe1EC2 (10 mg/kg/day, orally) for 4 months. SMe1EC2 ameliorated body weight loss, but not hyperglycemia of aged diabetic rats. Diabetes resulted in decreased glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD) and glutathione-S-transferase (GST), yet in unchanged glutathione reductase (GR) in the liver of aged diabetic rats. In the liver of the aged control rats, SMe1EC2 did not affectPublication Open Access COL4A1-related autosomal recessive encephalopathy in 2 Turkish children(Lippincott Williams and Wilkins (LWW), 2020) Yaramış, Ahmet; Lochmueller, Hanns; Topf, Ana; Sönmezler, Ece; Yılmaz, Elmasnur; Hız, Semra; Yiş, Uluç; Güngör, Serdal; Polat, Ayşe İpek; Edem, Pınar; Beltran, Sergi; Laurie, Steven; Horvath, Rita; Oktay, Yavuz; Yaramış, Ayşenur; Graduate School of Health SciencesObjective: this study presents the neurologic phenotypes of 2 brothers with a novel homozygous COL4A1 mutation that was identified in a large Turkish consanguineous cohort of neurogenetic diseases. Methods: whole-exome sequencing and bioinformatic analysis of consanguineous families with children affected by early-onset, neurogenetic disorders was performed using the RD-Connect Genome-Phenome Analysis Platform. We also performed clinical, EEG, and neuroimaging analyses in unaffected siblings and parents. Results: we have identified a homozygous missense mutation in COL4A1 (p.Gly1278Ser, NM-001845.5:c.3832G>T) in 2 siblings affected by small vessel brain disease with periventricular leukoencephalopathy and ocular defects. Presenting symptoms included mild weakness, hemiparetic gait, pyramidal findings, and seizures, whereas their intellectual and behavioral functions were normal. Both parents and 5 of the siblings (3 boys and 2 girls) were heterozygous for the variant. They did not show any clinical or laboratory signs of small vessel disease. Conclusions: COL4A1 has previously been associated with dominant small vessel disease of the brain and other organs, manifesting with high penetrance in heterozygous mutation carriers. Our findings provide evidence that COL4A1-related encephalopathy can be inherited in an autosomal recessive manner, which is important for counseling, prognosis, and treatment. Genotype-phenotype correlations remain to be established.Publication Open Access Comparison of multichannel intraluminal impedance-pH monitoring and reflux scintigraphy in pediatric patients with suspected gastroesophageal reflux(Baishideng Publishing Group (BPG), 2016) Bozkurt, Murat Fani; Temizel, İnci Nur Saltık; Demir, Hülya; Yüce, Aysel; Caner, Biray; Özen, Hasan; N/A; Kızılkan, Nuray Uslu; Faculty Member; School of MedicineAIM To evaluate the agreement of multichannel intraluminal impedance-pH monitoring (MII-pHM) and gastroesophageal reflux scintigraphy (GES) for the diagnosis of gastroesophageal reflux disease. METHODS Seventy-five consecutive patients with suspected gastroesophageal reflux disease (GERD) underwent 24-h combined MII-pHM recording and one hour radionuclide scintigraphy during the course of the MII-pHM study. Catheters with 6 impedance channels and 1 pH sensor were placed transnasally. Impedance and pH data analysis were performed automatically and manually. For impedance monitoring, reflux was defined as a retrograde 50% drop in impedance, starting distally and propagating retrogradely to at least the next two more proximal measuring channels. Reflux index (RI, percentage of the entire record that esophageal pH is < 4.0) greater than 4.2% for pHM and number of refluxes more than 50 for 24 h for MII were accepted as positive test results. At scintigraphy, 240 frames of 15 seconds duration were acquired in the supine position. Gastroesophageal reflux was defined as at least one reflux episode in the esophagus. After scintigraphic evaluation, impedance-pH recordings and scintigraphic images were evaluated together and agreement between tests were evaluated with Cohen's kappa. RESULTS Sufficient data was obtained from 60 (80%) patients (34 male, 56.7%) with a mean age of 8.7 +/- 3.7 years (range: 2.5-17.3 years; median: 8.5 years). Chronic cough, nausea, regurgitation and vomiting were the most frequent symptoms. The mean time for recording of MII-pHM was 22.8 +/- 2.4 h (range: 16-30 h; median: 22.7 h). At least one test was positive in 57 (95%) patients. According to diagnostic criteria, GERD was diagnosed in 34 (57.7%), 44 (73.3%), 47 (78.3%) and 51 (85%) patients by means of pHM, MII, GES and MII-pHM, respectively. The observed percentage agreements/kappa values for GES and pHM, GES and MII, GES and MII-pHM, and MII and pHM are 48.3%/-0.118; 61.7%/-0.042; 73.3%/0.116 and 60%/0.147, respectively. There was no or slight agreement between GES and pHM alone, MII alone or MII-pHM. pH monitoring alone missed 17 patients compared to combined MII-pHM. The addition of MII to pH monitoring increased the diagnosis rate by 50%. CONCLUSION No or slight agreement was found among pH monitoring, MII monitoring, MII-pH monitoring and GES for the diagnosis of gastroesophageal reflux disease.Publication Open Access Data reduction methods for ektacytometry in clinical hemorheology(IOS Press, 2013) Meiselman, Herbert J.; Başkurt, Oğuz Kerim; Faculty Member; School of Medicine; 2389Laser-diffraction ektacytometry is a generally accepted technique for measuring RBC deformability induced by fluid shear stress (SS) and yields paired elongation index-SS data at several levels of stress. Unfortunately, comparison of results is hindered by the lack of simple indices that accurately characterize these data. Several mathematical models have been proposed, including those developed for analysis of enzyme kinetics (Lineweaver-Burk, Eadie-Hofstee) and curve fitting (Streekstra-Bronkhorst). All of these analytical approaches provide a value for cell deformation at infinite stress (EImax) and the shear stress required to achieve one-half of this deformation (SS1/2); the use of non-linear regression is essential when calculating these parameters. While the current models provide equivalent results for normal RBC if used with non-linear regression, EImax and SS1/2 are not always concordant for cells with abnormal mechanical behavior. This technical note examines such differences for three conditions: glutaraldehyde treatment, mechanical stress and non-isotonic media. It was found that none of the models yield completely satisfactory values for EImax and SS1/2, especially if there are large changes of EImax. However, the ratio of SS1/2 to EImax (SS1/2/EImax) is much less affected by these problems, has similar power (i.e., standardized difference) as SS1/2 and EImax and is more robust in reflecting alterations of deformability. We thus conclude that the SS1/2/EImax ratio can be used when reporting and comparing various populations of RBC or cells obtained from subjects having different clinical states.Publication Open Access Development of small molecule MEIS inhibitors that modulate HSC activity(Nature Publishing Group (NPG), 2020) Turan, R.D.; Albayrak, E.; Uslu, M.; Siyah, P.; Alyazıcı, L.Y.; Aslan, G.S.; Yücel, D.; Aksöz, M.; Tüysüz, E.C.; Meriç, N.; Durdağı, S.; Gülbaş, Z.; Kocabaş, F.; Kalkan, Batuhan Mert; Graduate School of Health SciencesMeis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34l°w cells) and human (CD34+, CD133+, and ALDHhi cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1α, Hif-2α and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.Publication Open Access Effect of interferon alfa-2a treatment on adaptive and innate immune systems in patients with Behçet disease uveitis(Association for Research in Vision and Ophthalmology (ARVO), 2019) Oray, Merih; Kırımlı, Günay Uludağ; Gül, Ahmet; Tuğal-Tutkun, İlknur; Albayrak, Özgür; Can, Füsun; Önal, Sumru; Faculty Member; Other; Graduate School of Health Sciences; School of Medicine; Koç University Hospital; N/A; 103165; 52359Purpose: to investigate the effect of interferon alfa-2a on T regulatory (Treg) cells, T helper 17 (Th17) cells, and expression of Toll-like receptors (TLRs) in Behçet disease (BD) patients with uveitis. Methods: twenty-seven patients who received interferon alfa-2a for active BD uveitis despite conventional immunomodulatory therapies and healthy controls were enrolled. Peripheral blood Treg and Th17 cell frequencies were determined by flow cytometry as gated cells for CD3 + CD4 + Foxp3 + and CD3 + CD4 + IL17A + , respectively. Th17 RAR-related orphan receptor (ROR)γt mRNA expression was verified by real-time PCR (RT-PCR). Treg and Th17 cell cytokines were detected by ELISA in the supernatant of short-term cell cultures. RT-PCR was used to assess expression of TLR-2, TLR-3, TLR-4, TLR-8, and TLR-9 using cDNA prepared from CD4 + T cells and monocytes. Results: Treg and Th17 cell frequencies and Th17 RORγt expression were significantly elevated, and IL-10 concentration in Treg cell supernatants was significantly lower in BD patients than in controls. Th17 IL-17, IL-6, IL-21, IL-22, IL-23, IFN-γ, and TNF-α concentrations were significantly higher and all TLR expressions were significantly elevated in patients. Interferon alfa-2a led to a significant reversal in Treg and Th17 cell frequencies, Th17 RORγt expression, Treg and Th17 cell cytokine production, and TLR expression by CD4 + T cells and monocytes. Conclusions: despite a relative increase in Treg cells, impaired IL-10 production suggests that Treg dysfunction may play a role in induction of BD uveitis. Favorable effects of interferon alfa-2a may be associated with recovery of Treg cell function, suppression of Th17 cells, and reduced expression of TLRs on CD4 + T cells and monocytes.Publication Open Access Final Gleason score prediction using discriminant analysis and support vector machine based on preoperative multiparametric MR imaging of prostate cancer at 3T(Hindawi, 2014) Çıtak-Er, Füsun; Vural, Metin; Onay, Aslıhan; Öztürk-Işık, Esin; N/A; Esen, Tarık; Faculty Member; School of Medicine; 50536Objective. This study aimed at evaluating linear discriminant analysis (LDA) and support vector machine (SVM) classifiers for estimating final Gleason score preoperatively using multiparametric magnetic resonance imaging (mp-MRI) and clinical parameters. Materials and Methods. Thirty-three patients who underwent mp-MRI on a 3T clinical MR scanner and radical prostatectomy were enrolled in this study. The input features for classifiers were age, the presence of a palpable prostate abnormality, prostate specific antigen (PSA) level, index lesion size, and Likert scales of T2 weighted MRI (T2w-MRI), diffusion weighted MRI (DW-MRI), and dynamic contrast enhanced MRI (DCE-MRI) estimated by an experienced radiologist. SVM based recursive feature elimination (SVM-RFE) was used for eliminating features. Principal component analysis (PCA) was applied for data uncorrelation. Results. Using a standard PCA before final Gleason score classification resulted in mean sensitivities of 51.19% and 64.37% andmean specificities of 72.71% and 39.90% for LDA and SVM, respectively. Using a Gaussian kernel PCA resulted in mean sensitivities of 86.51% and 87.88% and mean specificities of 63.99% and 56.83% for LDA and SVM, respectively. Conclusion. SVM classifier resulted in a slightly higher sensitivity but a lower specificity than LDA method for final Gleason score prediction for prostate cancer for this limited patient population.Publication Open Access Immune profiling after minimally invasive lobectomy(Oxford University Press (OUP), 2020) Kapdağlı, Murat Hüseyin; Cesur, Ekin Ezgi; Erus, Suat; Öztürk, Ayşe Bilge; Albayrak, Özgür; İncir, Said; Yavuz, Ömer; Tanju, Serhan; Dilege, Şükrü; Faculty Member; Faculty Member; Faculty Member; Teaching Faculty; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Koç University Hospital; 175565; 147629; N/A; N/A; N/A; 214690; N/AObjectives: Whether acute phase and immune responses are minimally affected following minimally invasive lung surgery needs further investigation. We performed a pilot study to evaluate the immune profile of patients who underwent video-assisted thoracoscopic surgery or robot-assisted thoracic surgery lobectomies for the treatment of suspicious or known stage I non-small-cell lung cancer. Methods: blood samples were taken preoperatively and 3 and 24 h postoperatively were analysed for C-reactive protein, glucose, cortisol, tumour necrosis factor alpha (TNF-α), interleukin 8 (IL-8) and interleukin 10 (IL-10) levels. TNF-α, IL-8 and IL-10 were also measured in lung tissues. T (CD4, CD8), B (CD19) and natural killer (CD56, CD16) cell counts and natural killer cell functions were analysed using a flow cytometry-based assay before and after surgery. Results: minimally invasive surgery (robot-assisted thoracic surgery + video-assisted thoracoscopic surgery) significantly decreased IL-10 (P = 0.016) levels after surgery. No significant differences were detected in TNF-α (P = 0.48) and IL-8 (P = 0.15) levels before and after surgery. C-reactive protein (P < 0.001), cortisol (P < 0.001) and glucose levels (P < 0.001) increased significantly after surgery. Lymphocyte, total T cell, CD3+CD4+ and CD3+CD8+ CD16+CD56+ cell counts were significantly lower on postoperative day 1. Conclusion: there seems to be a dynamic balance between pro- and anti-inflammatory cytokines and immune cells following minimally invasive lobectomy.
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