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Öğe Biomarkers in hodgkin’s lymphoma(CRC Press, 2014) Demir, Esin; Yılmaz, Burak; Gündüz, Mehmet; Gündüz, EsraLymphoma is a type of hematological cancer which occurs in the immune system, and specifically starts in lymphocytes. Lymphoma is basically of two types: Hodgkin’s and non-Hodgkin’s lymphoma (NHL). This chapter will specifically focus on Hodgkin’s lymphoma (HL), whose subtypes are nodular lymphocyte-predominant Hodgkin’s lymphoma (NLPHL) and classical Hodgkin’s lymphoma (cHL). The characteristic cell types involved in these subtypes are different from each other. Biomarkers are another critical factor in making the correct identification of each subtype. Biomarkers can be categorized into different groups such as origin-related, chromosomal, cytokine, chemokine, and some important pathways-related markers. These biomarkers are not only important to distinguish subtypes but also critical to determine further treatment strategies for disease. Due to the importance of biomarker knowledge, we have reviewed significant HL biomarkers in this chapter. © 2018 Elsevier B.V., All rights reserved.Öğe Breast cancer stem cells and cellomics(Springer India, 2014) Demir, Esin; Atar, Bilge; Dhawan, Dipali; Barh, Debmalya; Gündüz, Mehmet; Gündüz, EsraOmics technologies are powerful high-throughput analytic tools to get inside whole-system level alterations of cancer cells. Since cancer stem cells are groups of vital cells in heterogeneous tumor populations, their omics analysis will enable better understanding in most controversial issues. These issues are mostly treatment resistance and metastatic ability of tumors. The relation between breast cancer patients' survival rates and stem cells in breast tumor has revealed the significance of breast cancer stem cells. The high tumor-forming capacity of these stem cells makes it necessary to get more comprehensive insight about their biology. Genomics, proteomics, and epigenomics are helpful tools for this purpose. The general step of these high-throughput methods is the isolation of breast cancer stem cells based on specific markers. Another shared feature of these omics approaches is to use a large set of interested genes, transcripts, or proteins. In addition to these two common key features, the remaining experimental setups may change from one to another omics analysis. The outcome of these approaches can yield some signatures, which will be mostly critical for later therapeutic strategies. Taken altogether, omics approaches not only reveal comprehensive understanding about breast cancer stem cells but also open the doors to more effective targeted therapies. © 2015 Elsevier B.V., All rights reserved.Öğe Genetic background of the rhinologic diseases(Springer-Verlag Berlin Heidelberg, 2013) Gündüz, Mehmet; Üçtepe, Eyyüp; Gündüz, EsraRhinologic diseases have a very high prevalence worldwide. It is known now that many rhinologic diseases have a strong genetic background. Some formidable challenges still remain for these diseases. However, research in the field of genetics has made much progress over the last decade and is expected to advance even further in the near future, as increasingly powerful analytical tools are being developed to unlock the complexities of genetic diseases. Information on the genetics of allergic diseases is important not only for analyzing the molecular basis of these diseases but also for investigating new drugs. Today, there is a huge effort to understand the molecular basis of disease and to find new therapies. © 2015 Elsevier B.V., All rights reserved.Öğe Genetic Basis of Metastasis(Springer Science+Business Media, 2019) Moroski-Erkul, Catherine A.; Demir, Esin; Gündüz, Esra; Gündüz, MehmetThe variation between and among the many types of cancer presents a formidable challenge both to practicing clinicians and medical researchers. There are several characteristics that are common to all cancers such as unrestrained proliferation and evasion of cell death. Another common feature is that of metastasis. Metastasis is “initiated” when primary tumor cells acquire the ability to invade surrounding tissues and eventually develop secondary tumors in distant locations. This process appears to rely not only on changes at the genetic level of tumor cells themselves but also from their interaction with surrounding stromal cells and the immune system. The genetic and molecular changes that give rise to metastatic change are of special interest due to the significant decline in a patient’s prognosis after metastasis has occured. A host of genes and pathways involved in several pathways have been implicated in this process, several of which will be reviewed in detail. © 2025 Elsevier B.V., All rights reserved.Öğe Investigation Of The Expression Of Rif1 Gene On Head And Neck, Pancreatic And Brain Cancer And Cancer Stem Cells(The Canadian Society for Clinical Investigation, 2016) Cila, Hacer E.Gurses; Acar, Muradiye; Barut, Furkan B.; Gündüz, Mehmet; Grènman, Reidar A.; Gündüz, EsraAbstract Purpose: Recent studies have shown that cancer stem cells are resistant to chemotherapy. The aim of this study was to compare RIF1 gene expression in head and neck, pancreatic cancer and glioma cell lines and the cancer stem cells isolated from these cell lines. Methods: UT-SCC-74 from Turku University and UT-SCC-74B primary tumor metastasis and neck cancer cell lines, YKG-1 glioma cancer cell line from RIKEN, pancreatic cancer cell lines and ASPC-1 cells from ATCC were grown in cell culture. To isolate cancer stem cells, ALDH-1 for UT-SCC-74 and UT-SCC-74B cell line, CD-133 for YKG-1 cell line and CD-24 for ASPC-1 cell line, were used as markers of cancer stem cells. RNA isolation was performed for both cancer lines and cancer stem cells. RNAs were converted to cDNA. RIF1 gene expression was performed by qRT-PCR analysis. RIF1 gene expression was compared with cancer cell lines and cancer stem cells isolated from these cell lines. The possible effect of RIF1 gene was evaluated. Results: In the pancreatic cells, RIF1 gene expression in the stem cell-positive cell line was 256 time that seen in the stem cell-negative cell line. Conclusion: Considering the importance of RIF1 in NHEJ and of NHEJ in pancreatic cancer, RIF1 may be one of the genes that plays an important role in the diagnoses and therapeutic treatment of pancreatic cancer. The results of head and neck and brain cancers are inconclusive and further studies are required to elucidate the connection between RIF1 gene and these other types of cancers © 2022 Elsevier B.V., All rights reserved.Öğe Omics of hereditary breast cancer(Springer India, 2014) Moroski-Erkul, Catherine A.; Yılmaz, Burak; Gündüz, Esra; Gündüz, MehmetBreast cancer is the leading cause of cancer-related deaths among women worldwide. Although advances in our understanding of this disease have been made in the last decade, the available treatments remain inadequate, particularly for the more intractable forms of breast cancer. Hereditary or familial breast cancer poses a particularly difficult challenge as only a few susceptibility genes with high penetrance have been identified, namely, BRCA1 and BRCA2. It is now suspected that the majority of hereditary and familial breast cancers are caused by various combinations of several moderate- and/or low-penetrance genes. Recent developments in research methodologies and conceptual frameworks within biology have revolutionized the study of cancer. This systems approach, which emphasizes a holistic understanding of biological systems, is referred to generally as omics. A decade of omics research has led to the identification of many new therapeutic targets and biomarkers, allowing for more accurate and earlier diagnosis and treatment of the wide spectrum of diseases that are collectively referred to as breast cancer. Here we review the contributions of several omics fields to our understanding of hereditary and familial breast cancer, namely, genomics, transcriptomics, proteomics, and metabolomics. © 2015 Elsevier B.V., All rights reserved.Öğe Omics of male breast cancer(Springer India, 2014) Ünal, Zahide Nur; Kaya, Gülhan; Barh, Debmalya; Gündüz, Esra; Gündüz, MehmetMale breast cancer (MBC) is rarely diagnosed. However, it has relatively poor prognosis when compared to female breast cancer. Although the importance of genetic predisposition in MBC etiology has been considerably understood, a wide range of gene and protein alterations playing various roles in MBC carcinogenesis point at its polygenic nature rather than single gene inheritance. Therefore, more comprehensive approaches including omics study and related technologies are required to thoroughly manage this malignancy, though such studies have been scarcely performed in MBC. © 2015 Elsevier B.V., All rights reserved.Öğe Oncogenes and tumor suppressor genes as a biomarker in breast cancer(Springer India, 2014) Üçtepe, Eyyüp; Acar, Muradiye; Gündüz, Esra; Gündüz, MehmetBreast cancer is the most common cause of cancer in women in the United States and the Western world. The important question is what can be done to limit the human suffering associated with cancer and to reduce the burden on society? One solution is early detection. Early diagnosis of breast cancer before symptoms emerge is the most effective prevention of breast cancer. Currently, mammography is the gold standard for breast cancer screening. The procedure is suggested and often reimbursed for women between the ages of 50 and 75. Yet it is presumed that between 15 and 25 % of women with early-stage breast cancers are presently missed by commonly used diagnostic procedures such as mammography. Since breast cancer is also diagnosed in an increasing number of younger women, the screening strategy should be modified. Hence, oncogenes and tumor suppressor genes could be used as biomarkers for early detection of breast cancer. Eventually, researchers aim to use the molecular data collected from an individual tumor for prognostication and personalized therapy for each patient. Genetic profiles of tumors are now providing information about clinical outcome, and some prognostic and predictive indicators have appeared based on this research. In the near future, prospective tissue collection for molecular analysis may become routine in order to classify patients for alternative treatment options and to optimize treatment strategies based on molecular structure of the cancer. © 2015 Elsevier B.V., All rights reserved.Öğe Pharmaco-epigenomics(Springer India, 2013) Gündüz, Mehmet; Acar, Muradiye; Erdogan, Kubra; Cetin, Elif Nihan; Gündüz, EsraEpigenetic modifications are defined as the study of heritable changes in phenotype that do not involve alterations in the DNA sequence. DNA methylation, posttranslational modifi cations of the histone proteins, and miRNAs are regulating the expression of genes as well as drug- metabolizing genes. Epigenetic regulation is essential for normal developmental and cellular processes. Conversely, abnormal epigenetic regulation is a character of complex diseases, including cancer, hematological malignancies, psychiatric disorders, and other diseases. Pharmaco-epigenomics is a novel discipline and involves the study of epigenetic factors in the interpersonal variation to drugs. Epigenetic biomarkers can be used to diagnose disease, estimate disease progression, or predict interpersonal variations in response to therapy. Unlike genetic alterations, changes in epigenetic machinery are reversible, and this reversible characteristic makes them an attractive therapeutic targets. © 2018 Elsevier B.V., All rights reserved.Öğe Pharmacogenomics in acute myeloid leukemia(Springer India, 2013) Hatipoğlu, Ömer Faruk; Bender, Onur; Gündüz, Esra; Gündüz, MehmetAcute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells. In AML, the bone marrow makes many immature cells called blasts, which do not mature and cannot fi ght infections. AML is a heterogeneous neoplasm with several pathological, genetic, and molecular subtypes. Combinations of various doses and schedules of drugs have been the majority of treatment for all types of AMLs in adult patients. However, not all patients have the same response to these treatments, some of which are adverse responses that are potentially life threatening. Because interindividual responses to AML medications can vary considerably, the potential for genetic contributions to variable drug responses is signifi cant. The pharmacogenomics approach tries to fi nd prognostic and predictive biomarkers permitting to identify patients who could benefi t from a particular treatment or those exhibiting higher risks of toxicity. Pharmacogenomics is a rapidly improving science with the potential to revolutionize drug discovery/development and offers one possibility for rationalizing therapy/dose selection. It combines many different fi elds such as genetics, genomics, molecular biology, pharmacology, pharmaceutics, and population biology. This chapter focuses on treatment of AML, genetic and clinical prognostic markers, and recent advances in the fi eld of pharmacogenomics in AML. © 2016 Elsevier B.V., All rights reserved.Öğe Precision medicine in oncology: An overview(CRC Press, 2018) Yilmaz, Fazilet G.; Yilmaz, Sultan Ciftci; Gündüz, Esra; Gündüz, Mehmet[No abstract available]Öğe Suppression Of Bromodomaincontaining Protein 4 By Shrna: A New Approach For Cancer Treatment(The Canadian Society for Clinical Investigation, 2016) Kaya, Turan; Kahraman, Berke; Bazarov, Nurgeldi; Toker, Alperen S.; Celik, Ayse; Cigdem, Sadik; Gündüz, EsraPurpose: MYC is a transcription factor coding gene that is believed to control 15% of the genes in the entire human genome. The central role of c-MYC in cancer pathogenesis makes it a major therapeutic target in field of anticancer agent development. Methods: We targeted the acetyl-lysine binding modules or bromodomains, which are associated with c-MYC transcriptional activation. Results: Sequence specific inhibition of BET bromodomains with small hairpin RNAs (shRNAs) resulted in cessation of cellular proliferation in different cancer cell lines. Unlike previous studies on inhibition of bromodomains with selective small-molecule inhibitors, our study revealed the significant role of BET bromodomains in solid tumours and also highlighted the ease of RNA interference (RNAi) methodology for inhibition of bromodomain translation. Conclusion: The degree of influence of BET bromodomain inhibition on proliferation in five cancer cell lines established it as the major target in malignancies characterized by activation of c-MYC © 2021 Elsevier B.V., All rights reserved.
