Browsing by Author "Banerjee, S."
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Item Open Access 15-Lipoxygenase-1 re-expression in colorectal cancer alters endothelial cell features through enhanced expression of TSP-1 and ICAM-1(Elsevier, 2017-11) Tunçer, S.; Keşküş, A. G.; Çolakoğlu, M.; Çimen, I.; Yener, C.; Konu, Ö.; Banerjee, S.15-lipoxygenase-1 (15-LOX-1) oxygenates linoleic acid to 13(S)-hydroxyoctadecadienoic acid (HODE). The enzyme is widely suppressed in different cancers and its re-expression has tumor suppressive effects. 15-LOX-1 has been shown to inhibit neoangiogenesis in colorectal cancer (CRC); in the present study we confirm this phenomenon and describe the mechanistic basis. We show that re-expression of 15-LOX-1 in CRC cell lines resulted in decreased transcriptional activity of HIF1α and reduced the expression and secretion of VEGF in both normoxic and hypoxic conditions. Conditioned medium (CM) was obtained from CRC or prostate cancer cell lines re-expressing 15-LOX-1 (15-LOX-1CM). 15-LOX-1CM treated aortic rings from 6-week old C57BL/6 mice showed significantly less vessel sprouting and more organized structure of vascular network. Human umbilical vein endothelial cells (HUVECs) incubated with 15-LOX-1CM showed reduced motility, enhanced expression of intercellular cell adhesion molecule (ICAM-1) and reduced tube formation but no change in proliferation or cell-cycle distribution. HUVECs incubated with 13(S)-HODE partially phenocopied the effects of 15-LOX-1CM, i.e., showed reduced motility and enhanced expression of ICAM-1, but did not reduce tube formation, implying the importance of additional factors. Therefore, a Proteome Profiler Angiogenesis Array was carried out, which showed that Thrombospondin-1 (TSP-1), a matrix glycoprotein known to strongly inhibit neovascularization, was expressed significantly more in HUVECs incubated with 15-LOX-1CM. TSP-1 blockage in HUVECs reduced the expression of ICAM-1 and enhanced cell motility, thereby providing a mechanism for reduced angiogenesis. The anti-angiogenic effects of 15-LOX-1 through enhanced expressions of ICAM-1 and TSP-1 are novel findings and should be explored further to develop therapeutic options.Item Open Access Diffusion tensor imaging and T2 relaxometry of bilateral lumbar nerve roots: feasibility of in‐plane imaging(Wiley, 2013) Karampinos, D.; Melkus, G.; Shepherd, T.; Banerjee, S.; Sarıtaş, Emine Ülkü; Shankaranarayanan, A.; Hess, C.; Link, T.; Dillon, W.; Majumdar, S.Lower back pain is a common problem frequently encountered without specific biomarkers that correlate well with an individual patient's pain generators. MRI quantification of diffusion and T2 relaxation properties may provide novel insight into the mechanical and inflammatory changes that occur in the lumbosacral nerve roots in patients with lower back pain. Accurate imaging of the spinal nerve roots is difficult because of their small caliber and oblique course in all three planes. Two‐dimensional in‐plane imaging of the lumbosacral nerve roots requires oblique coronal imaging with large field of view (FOV) in both dimensions, resulting in severe geometric distortions using single‐shot echo planar imaging (EPI) techniques. The present work describes initial success using a reduced‐FOV single‐shot spin‐echo EPI acquisition to obtain in‐plane diffusion tensor imaging (DTI) and T2 mapping of the bilateral lumbar nerve roots at the L4 level of healthy subjects, minimizing partial volume effects, breathing artifacts and geometric distortions. A significant variation in DTI and T2 mapping metrics is also reported along the course of the normal nerve root. The fractional anisotropy is statistically significantly lower in the dorsal root ganglia (0.287 ± 0.068) than in more distal regions in the spinal nerve (0.402 ± 0.040) (p < 10–5). The T2 relaxation value is statistically significantly higher in the dorsal root ganglia (78.0 ± 11.9 ms) than in more distal regions in the spinal nerve (59.5 ± 7.4 ms) (p < 10–5). The quantification of nerve root DTI and T2 properties using the proposed methodology may identify the specific site of any degenerative and inflammatory changes along the nerve roots of patients with lower back pain..Item Open Access Enhanced expression of HNF4α during intestinal epithelial differentiation is involved in the activation of ER stress(Wiley, 2020) Tunçer, S.; Sade-Memişoğlu, A.; Keşküş, Ayşe Gökçe; Sheraj, I.; Sheraj, G.; Akyol, G.; Banerjee, S.Intestinal epithelial cells are derived from stem cells at the crypts that undergo differentiation into transit‐amplifying cells, which in turn form terminally differentiated enterocytes as these cells reach the villus. Extensive alterations in both transcriptional and translational programs occur during differentiation, which can induce the activation of cellular stress responses such as ER stress‐related unfolded protein response (UPR) and autophagy, particularly in the cells that are already committed to becoming absorptive cells. Using an epithelial cell model of enterocyte differentiation, we report a mechanistic study connecting enterocyte differentiation to UPR and autophagy. We report that differentiated colon epithelial cells showed increased cytosolic Ca2+ levels and activation of all three pathways of UPR: inositol‐requiring enzyme 1 (IRE1), protein kinase RNA‐like ER kinase, and activating transcription factor 6 (ATF6) compared to the undifferentiated cells. Enhanced UPR in the differentiated cells was accompanied by the induction of autophagy as evidenced by increased ratio of light chain 3 II/I, upregulation of Beclin‐1, and downregulation of p62. We show for the first time that mechanistically, the upregulation of hepatocyte nuclear factor 4α (HNF4α) during differentiation led to increased promoter binding and transcriptional upregulation of two major proteins of UPR: X‐box binding protein‐1 and ATF6, implicating HNF4α as a key regulator of UPR response during differentiation. Integrating wet‐lab with in silico analyses, the present study links differentiation to cellular stress responses, and highlights the importance of transcription factor signaling and cross‐talk between the cellular events in the regulation of intestinal cell differentiation.Item Open Access Epigenetic Mechanisms Underlying the Dynamic Expression of Cancer-Testis Genes, PAGE2,-2B and SPANX-B, during Mesenchymal-to-Epithelial Transition(pone, 2014) Yilmaz Ozcan, S.; Sade, A.; Kucukkaraduman, B.; Kaygusuz, Y.; Senses, K. M.; Banerjee, S.; Gure, A. O.Cancer-testis (CT) genes are expressed in various cancers but not in normal tissues other than in cells of the germline. Although DNA demethylation of promoter-proximal CpGs of CT genes is linked to their expression in cancer, the mechanisms leading to demethylation are unknown. To elucidate such mechanisms we chose to study the Caco-2 colorectal cancer cell line during the course of its spontaneous differentiation in vitro, as we found CT genes, in particular PAGE2,-2B and SPANX-B, to be up-regulated during this process. Differentiation of these cells resulted in a mesenchymal-toepithelial transition (MET) as evidenced by the gain of epithelial markers CDX2, Claudin-4 and E-cadherin, and a concomitant loss of mesenchymal markers Vimentin, Fibronectin-1 and Transgelin. PAGE2 and SPAN-X up-regulation was accompanied by an increase in Ten-eleven translocation-2 (TET2) expression and cytosine 5-hydroxymethylation as well as the disassociation of heterochromatin protein 1 and the polycomb repressive complex 2 protein EZH2 from promoter-proximal regions of these genes. Reversal of differentiation resulted in down-regulation of PAGE2,-2B and SPANX-B, and induction of epithelial-to-mesenchymal transition (EMT) markers, demonstrating the dynamic nature of CT gene regulation in this model. © 2014 Yilmaz-Ozcan et al.Item Open Access Evaluation of an aldo-keto reductase gene signature with prognostic significance in colon cancer via activation of epithelial to mesenchymal transition and the p70S6K pathway(Oxford University Press, 2020-07) Demirkol Canlı, S.; Seza, E. G.; Sheraj, I.; Gömçeli, İ.; Turhan, N.; Carberry, S.; Prehn, J. H. M.; Güre, Ali Osmay; Banerjee, S.AKR1B1 and AKR1B10, members of the aldo-keto reductase family of enzymes that participate in the polyol pathway of aldehyde metabolism, are aberrantly expressed in colon cancer. We previously showed that high expression of AKR1B1 (AKR1B1HIGH) was associated with enhanced motility, inflammation and poor clinical outcome in colon cancer patients. Using publicly available datasets and ex vivo gene expression analysis (n = 51, Ankara cohort), we have validated our previous in silico finding that AKR1B1HIGH was associated with worse overall survival (OS) compared with patients with low expression of AKR1B1 (AKR1B1LOW) samples. A combined signature of AKR1B1HIGH and AKR1B10LOW was significantly associated with worse recurrence-free survival (RFS) in microsatellite stable (MSS) patients and in patients with distal colon tumors as well as a higher mesenchymal signature when compared with AKR1B1LOW/AKR1B10HIGH tumors. When the patients were stratified according to consensus molecular subtypes (CMS), AKR1B1HIGH/AKR1B10LOW samples were primarily classified as CMS4 with predominantly mesenchymal characteristics while AKR1B1LOW/AKR1B10HIGH samples were primarily classified as CMS3 which is associated with metabolic deregulation. Reverse Phase Protein Array carried out using protein samples from the Ankara cohort indicated that AKR1B1HIGH/AKR1B10LOW tumors showed aberrant activation of metabolic pathways. Western blot analysis of AKR1B1HIGH/AKR1B10LOW colon cancer cell lines also suggested aberrant activation of nutrient-sensing pathways. Collectively, our data suggest that the AKR1B1HIGH/AKR1B10LOW signature may be predictive of poor prognosis, aberrant activation of metabolic pathways, and can be considered as a novel biomarker for colon cancer prognostication.Item Open Access Opposing roles of the aldo-keto reductases AKR1B1 and AKR1B10 in colorectal cancer(Springer Netherlands, 2017-09) Taskoparan, B.; Seza, E. G.; Demirkol, S.; Tuncer, S.; Stefek, M.; Gure, A. O.; Banerjee, S.Purpose: Aldo-keto reductases (including AKR1B1 and AKR1B10) constitute a family of oxidoreductases that have been implicated in the pathophysiology of diabetes and cancer, including colorectal cancer (CRC). Available data indicate that, despite their similarities in structure and enzymatic functions, their roles in CRC may be divergent. Here, we aimed to determine the expression and functional implications of AKR1B1 and AKR1B10 in CRC. Methods: AKR1B1 and AKR1B10 gene expression levels were analyzed using publicly available microarray data and ex vivo CRC-derived cDNA samples. Gene Set Enrichment Analysis (GSEA), The Cancer Genome Atlas (TCGA) RNA-seq data and The Cancer Proteome Atlas (TCPA) proteome data were analyzed to determine the effect of high and low AKR1B1 and AKR1B10 expression levels in CRC patients. Proliferation, cell cycle progression, cellular motility, adhesion and inflammation were determined in CRC-derived cell lines in which these genes were either exogenously overexpressed or silenced. Results: We found that the expression of AKR1B1 was unaltered, whereas that of AKR1B10 was decreased in primary CRCs. GSEA revealed that, while high AKR1B1 expression was associated with increased cell cycle progression, cellular motility and inflammation, high AKR1B10 expression was associated with a weak inflammatory phenotype. Functional studies carried out in CRC-derived cell lines confirmed these data. Microarray data analysis indicated that high expression levels of AKR1B1 and AKR1B10 were significantly associated with shorter and longer disease-free survival rates, respectively. A combined gene expression signature of AKR1B10 (low) and AKR1B1 (high) showed a better prognostic stratification of CRC patients independent of confounding factors. Conclusions: Despite their similarities, the expression levels and functions of AKR1B1 and AKR1B10 are highly divergent in CRC, and they may have prognostic implications.Item Open Access Reduced field-of-view DWI with robust fat suppression and unrestricted slice coverage using tilted 2D RF excitation(John Wiley and Sons Inc., 2016) Banerjee, S.; Nishimura, D. G.; Shankaranarayanan, A.; Saritas, E. U.Purpose: Reduced field-of-view (rFOV) diffusion-weighted imaging (DWI) using 2D echo-planar radiofrequency (2DRF) excitation has been widely and successfully applied in clinical settings. The purpose of this work is to further improve its clinical utility by overcoming slice coverage limitations without any scan time penalty while providing robust fat suppression. Theory and Methods: During multislice imaging with 2DRF pulses, periodic sidelobes in the slice direction cause partial saturation, limiting the slice coverage. In this work, a tilting of the excitation plane is proposed to push the sidelobes out of the imaging section while preserving robust fat suppression. The 2DRF pulse is designed using Shinnar-Le Roux algorithm on a rotated excitation k-space. The performance of the method is validated via simulations, phantom experiments, and high in-plane resolution in vivo DWI of the spinal cord. Results: Results show that rFOV DWI using the tilted 2DRF pulse provides increased signal-to-noise ratio, extended coverage, and robust fat suppression, without any scan time penalty. Conclusion: Using a tilted 2DRF excitation, a high-resolution rFOV DWI method with robust fat suppression and unrestricted slice coverage is presented. This method will be beneficial in clinical applications needing large slice coverage, for example, axial imaging of the spine, prostate, or breast. Magn Reson Med 76:1668–1676, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine