Person: ARĞA, KAZIM YALÇIN
Loading...
Email Address
Birth Date
Research Projects
Organizational Units
Job Title
Last Name
ARĞA
First Name
KAZIM YALÇIN
Name
6 results
Search Results
Now showing 1 - 6 of 6
Publication Open Access Repositioning of anti-inflammatory drugs for the treatment of cervical cancer sub-types(2022-06-01) TURANLI, BESTE; ARĞA, KAZIM YALÇIN; Kori M., ARĞA K. Y., Mardinoglu A., TURANLI B.Cervical cancer is the fourth most commonly diagnosed cancer worldwide and, in almost all cases is caused by infection with highly oncogenic Human Papillomaviruses (HPVs). On the other hand, inflammation is one of the hallmarks of cancer research. Here, we focused on inflammatory proteins that classify cervical cancer patients by considering individual differences between cancer patients in contrast to conventional treatments. We repurposed anti-inflammatory drugs for therapy of HPV-16 and HPV-18 infected groups, separately. In this study, we employed systems biology approaches to unveil the diagnostic and treatment options from a precision medicine perspective by delineating differential inflammation-associated biomarkers associated with carcinogenesis for both subtypes. We performed a meta-analysis of cervical cancer-associated transcriptomic datasets considering subtype differences of samples and identified the differentially expressed genes (DEGs). Using gene signature reversal on HPV-16 and HPV-18, we performed both signature- and network-based drug reversal to identify anti-inflammatory drug candidates against inflammation-associated nodes. The anti-inflammatory drug candidates were evaluated using molecular docking to determine the potential of physical interactions between the anti-inflammatory drug and inflammation-associated nodes as drug targets. We proposed 4 novels anti-inflammatory drugs (AS-601245, betamethasone, narciclasin, and methylprednisolone) for the treatment of HPV-16, 3 novel drugs for the treatment of HPV-18 (daphnetin, phenylbutazone, and tiaprofenoic acid), and 5 novel drugs (aldosterone, BMS-345541, etodolac, hydrocortisone, and prednisolone) for the treatment of both subtypes. We proposed anti-inflammatory drug candidates that have the potential to be therapeutic agents for the prevention and/or treatment of cervical cancer.Publication Open Access Editorial: Omics integration and network medicine to decipher human complex diseases(2023-01-01) ARĞA, KAZIM YALÇIN; Zanfardino M., Babbi G., ARĞA K. Y., Pane K.Publication Open Access Potential early markers for breast cancer: a proteomic approach comparing saliva and serum samples in a pilot study(2023-02-01) ARĞA, KAZIM YALÇIN; Sinha I., Fogle R. L., Gulfidan G., Stanley A. E., Walter V., Hollenbeak C. S., ARĞA K. Y., Sinha R.Breast cancer is the second leading cause of death for women in the United States, and early detection could offer patients the opportunity to receive early intervention. The current methods of diagnosis rely on mammograms and have relatively high rates of false positivity, causing anxiety in patients. We sought to identify protein markers in saliva and serum for early detection of breast cancer. A rigorous analysis was performed for individual saliva and serum samples from women without breast disease, and women diagnosed with benign or malignant breast disease, using isobaric tags for relative and absolute quantitation (iTRAQ) technique, and employing a random effects model. A total of 591 and 371 proteins were identified in saliva and serum samples from the same individuals, respectively. The differentially expressed proteins were mainly involved in exocytosis, secretion, immune response, neutrophil-mediated immunity and cytokine-mediated signaling pathway. Using a network biology approach, significantly expressed proteins in both biological fluids were evaluated for protein–protein interaction networks and further analyzed for these being potential biomarkers in breast cancer diagnosis and prognosis. Our systems approach illustrates a feasible platform for investigating the responsive proteomic profile in benign and malignant breast disease using saliva and serum from the same women.Publication Open Access Three candidate anticancer drugs were repositioned by integrative analysis of the transcriptomes of species with different regenerative abilities after injury(2023-10-01) ARĞA, KAZIM YALÇIN; Kubat Oktem E., Demir U., Yazar M., ARGA K. Y.Regeneration is a homeostatic process that involves the restoration of cells and body parts. Most of the molecular mechanisms and signalling pathways involved in wound healing, such as proliferation, have also been associated with cancer cell growth, suggesting that cancer is an over/unhealed wound. In this study, we examined differentially expressed genes in spinal cord samples from regenerative organisms (axolotl and zebrafish) and nonregenerative organisms (mouse and rat) compared to intact control spinal cord samples using publicly available transcriptomics data and bioinformatics analyses. Based on these gene signatures, we investigated 3 small compounds, namely cucurbitacin I, BMS-754807, and PHA-793887 as potential candidates for the treatment of cancer. The predicted target genes of the repositioned compounds were mainly enriched with the greatest number of genes in cancer pathways. The molecular docking results on the binding affinity between the repositioned compounds and their target genes are also reported. The repositioned 3 small compounds showed anticancer effect both in 2D and 3D cell cultures using the prostate cancer cell line as a model. We propose cucurbitacin I, BMS-754807, and PHA-793887 as potential anticancer drug candidates. Future studies on the mechanisms associated with the revealed gene signatures and anticancer effects of these three small compunds would allow scientists to develop therapeutic approaches to combat cancer. This research contributes to the evaluation of mechanisms and gene signatures that either limit or cause cancer, and to the development of new cancer therapies by establishing a link between regeneration and carcinogenesis.Publication Open Access Integrative analysis of motor neuron and microglial transcriptomes from SOD1(G93A) mice models uncover potential drug treatments for ALS(2022-09-01) ARĞA, KAZIM YALÇIN; KUBAT ÖKTEM E., Aydin B., Yazar M., ARĞA K. Y.Amyotrophic lateral sclerosis (ALS) is a fatal disease of motor neurons that mainly affects the motor cortex, brainstem, and spinal cord. Under disease conditions, microglia could possess two distinct profiles, M1 (toxic) and M2 (protective), with the M2 profile observed at disease onset. SOD1 (superoxide dismutase 1) gene mutations account for up to 20% of familial ALS cases. Comparative gene expression differences in M2-protective (early) stage SOD1(G93A) microglia and age-matched SOD1(G93A) motor neurons are poorly understood. We evaluated the differential gene expression profiles in SOD1(G93A) microglia and SOD1(G93A) motor neurons utilizing publicly available transcriptomics data and bioinformatics analyses, constructed biomolecular networks around them, and identified gene clusters as potential drug targets. Following a drug repositioning strategy, 5 small compounds (belinostat, auranofin, BRD-K78930611, AZD-8055, and COT-10b) were repositioned as potential ALS therapeutic candidates that mimic the protective state of microglia and reverse the toxic state of motor neurons. We anticipate that this study will provide new insights into the ALS pathophysiology linking the M2 state of microglia and drug repositioning.Publication Open Access A cross-sectional study of biotechnology awareness and teaching in European high schools(2010-12-01) ARĞA, KAZIM YALÇIN; Vanderschuren H., Heinzmann D., Faso C., Stupak M., ARĞA K. Y., Hoerzer H., Laizet Y., Leduchowska P., Silva N., Simkova K.Undoubtedly, biotechnology has a tremendous impact on our daily lives As a result of this and in parallel to the advancement of knowledge in this field of applied research, consumer awareness of the potential benefits and risks of this technology has steadily increased, leading to a thorough investigation of the public perception of biotechnology in the past years Indeed, it has become clear that it is in the general interest of science and especially of applied research to inform the public of its advances A promising next step is to strengthen biotechnology communication in scholastic institutions In this paper, we investigate the perception of biotechnology in a specific target group, namely high-school students in the 16-20-year-old age range We conducted a questionnaire-based survey on a total of 1410 students in six European countries to investigate students\" perception, concern, scientific knowledge, and awareness Our data revealed some unexpected patterns of acceptance and concern about biotechnology Knowledge analysis indicated that pupils lack specific knowledge about biotechnological applications and their interest in biotechnology appeared to be linked to knowledge Analysis of specific questions about teaching practices at schools suggests that a better targeted choice in media as vehicles for information together with selected speakers could be instrumental in increasing students\" interest in science and more specifically in biotechnology