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2. Molecular Signatures in Acute Myeloid Leukemia: From Diagnosis to Targeted Therapy and Drug Repositioning

Author

Kelesoglu, Nurdan, Karademir-Yilmaz, Betul, Arga, Kazim Yalcin, Rezaei, Nima, Series Editor, Aguiar, Rodrigo, Editorial Board Member, Ahmed, Atif A., Editorial Board Member, Ambrosio, Maria R., Editorial Board Member, Artac, Mehmet, Editorial Board Member, Augustine, Tanya N., Editorial Board Member, Bambauer, Rolf, Editorial Board Member, Bhat, Ajaz Ahmad, Editorial Board Member, Bertolaccini, Luca, Editorial Board Member, Bianchini, Chiara, Editorial Board Member, Cavic, Milena, Editorial Board Member, Chakrabarti, Sakti, Editorial Board Member, Cho, William C. S., Editorial Board Member, Czarnecka, Anna M., Editorial Board Member, Domingues, Cátia, Editorial Board Member, Eşkazan, A. Emre, Editorial Board Member, Fares, Jawad, Editorial Board Member, Fonseca Alves, Carlos E., Editorial Board Member, Fru, Pascaline, Editorial Board Member, Da Gama Duarte, Jessica, Editorial Board Member, García, Mónica C., Editorial Board Member, Gener, Melissa A.H., Editorial Board Member, Estrada Guadarrama, José Antonio, Editorial Board Member, Hargadon, Kristian M., Editorial Board Member, Holvoet, Paul, Editorial Board Member, Jurisic, Vladimir, Editorial Board Member, Kabir, Yearul, Editorial Board Member, Katsila, Theodora, Editorial Board Member, Kleeff, Jorg, Editorial Board Member, Liang, Chao, Editorial Board Member, Tan, Mei Lan, Editorial Board Member, Li, Weijie, Editorial Board Member, Prado López, Sonia, Editorial Board Member, Macha, Muzafar A., Editorial Board Member, Malara, Natalia, Editorial Board Member, Orhan, Adile, Editorial Board Member, Prado-Garcia, Heriberto, Editorial Board Member, Pérez-Velázquez, Judith, Editorial Board Member, Rashed, Wafaa M., Editorial Board Member, Sanguedolce, Francesca, Editorial Board Member, Sorrentino, Rosalinda, Editorial Board Member, Shubina, Irina Zh., Editorial Board Member, de Araujo, Heloisa Sobreiro Selistre, Editorial Board Member, Torres-Suárez, Ana Isabel, Editorial Board Member, Włodarczyk, Jakub, Editorial Board Member, Yeong, Joe Poh Sheng, Editorial Board Member, Toscano, Marta A., Editorial Board Member, Wong, Tak-Wah, Editorial Board Member, Yin, Jun, Editorial Board Member, Yu, Bin, Editorial Board Member, and Hamdy, Nadia M., Editorial Board Member

Published
2024
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3. Unlocking the Power of Immune Microenvironment in AML Therapy: Current Insight and Future Prospects

Author

Kelesoglu, Nurdan, Arga, Kazim Yalcin, Rezaei, Nima, Series Editor, Aguiar, Rodrigo, Editorial Board Member, Ahmed, Atif A., Editorial Board Member, Ambrosio, Maria R., Editorial Board Member, Artac, Mehmet, Editorial Board Member, Augustine, Tanya N., Editorial Board Member, Bambauer, Rolf, Editorial Board Member, Bhat, Ajaz Ahmad, Editorial Board Member, Bertolaccini, Luca, Editorial Board Member, Bianchini, Chiara, Editorial Board Member, Cavic, Milena, Editorial Board Member, Chakrabarti, Sakti, Editorial Board Member, Cho, William C. S., Editorial Board Member, Czarnecka, Anna M., Editorial Board Member, Domingues, Cátia, Editorial Board Member, Eşkazan, A. Emre, Editorial Board Member, Fares, Jawad, Editorial Board Member, Fonseca Alves, Carlos E., Editorial Board Member, Fru, Pascaline, Editorial Board Member, Da Gama Duarte, Jessica, Editorial Board Member, García, Mónica C., Editorial Board Member, Gener, Melissa A.H., Editorial Board Member, Estrada Guadarrama, José Antonio, Editorial Board Member, Hargadon, Kristian M., Editorial Board Member, Holvoet, Paul, Editorial Board Member, Jurisic, Vladimir, Editorial Board Member, Kabir, Yearul, Editorial Board Member, Katsila, Theodora, Editorial Board Member, Kleeff, Jorg, Editorial Board Member, Liang, Chao, Editorial Board Member, Tan, Mei Lan, Editorial Board Member, Li, Weijie, Editorial Board Member, Prado López, Sonia, Editorial Board Member, Macha, Muzafar A., Editorial Board Member, Malara, Natalia, Editorial Board Member, Orhan, Adile, Editorial Board Member, Prado-Garcia, Heriberto, Editorial Board Member, Pérez-Velázquez, Judith, Editorial Board Member, Rashed, Wafaa M., Editorial Board Member, Sanguedolce, Francesca, Editorial Board Member, Sorrentino, Rosalinda, Editorial Board Member, Shubina, Irina Zh., Editorial Board Member, de Araujo, Heloisa Sobreiro Selistre, Editorial Board Member, Torres-Suárez, Ana Isabel, Editorial Board Member, Włodarczyk, Jakub, Editorial Board Member, Yeong, Joe Poh Sheng, Editorial Board Member, Toscano, Marta A., Editorial Board Member, Wong, Tak-Wah, Editorial Board Member, Yin, Jun, Editorial Board Member, Yu, Bin, Editorial Board Member, and Hamdy, Nadia M., Editorial Board Member

Published
2024
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8. List of contributors

Author

Aboulmouhajir, Aziz, primary, Ahmed, Sheik S.S.J., additional, Alexandrova, Radostina, additional, Anouar Tadlaoui, Kaoutar, additional, Arga, Kazim Yalcin, additional, Barrijal, Said, additional, Baskar, Mahalakshmi, additional, Bastikar, Alpana, additional, Bastikar, Virupaksha Ajit, additional, Bazir, Hanaâ, additional, Benchekroun, Mohammed Nabil, additional, Bennani, Bahia, additional, Bessi, Hlima, additional, Bhaskar Kalarani, Iyshwarya, additional, Bothe, Santosh Ajabrao, additional, Bouchikhi, Benachir, additional, Byadi, Said, additional, Chhajed, Santosh Subhash, additional, Diouf, Alassane, additional, El Bari, Nezha, additional, El Battioui, Fadoua, additional, El Malki, Fatima, additional, Ennaji, Moulay Mustapha, additional, Ghazal, Hassan, additional, Gupta, Pramodkumar Pyarelal, additional, Hassou, Najwa, additional, Kaviarasan, Vaishak, additional, Kori, Medi, additional, Labyed, Marwah, additional, Motia, Soukaina, additional, Mzibri, Mohammed El, additional, Panwar, Harsh, additional, Podlipnik, Črtomir, additional, Pramasivam, Prabu, additional, Ragunath, Barath, additional, Salma, Elamrani Elhassani, additional, Saravanan, ChandraLekha, additional, Sudhan, Mookkandi, additional, Thasneem, Kamila, additional, and Veerabathiran, Ramakrishnan, additional

Published
2023
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10. Biomarkers From Discovery to Clinical Application: In Silico Pre-Clinical Validation Approach in the Face of Lung Cancer.

Author

Kori, Medi, Gov, Esra, Arga, Kazim Yalcin, and Sinha, Raghu

Subjects
TUMOR markers, LUNG cancer, PROTEIN engineering, BIOMARKERS, BRONCHOALVEOLAR lavage
Abstract

Background: Clinical biomarkers, allow better classification of patients according to their disease risk, prognosis, and/or response to treatment. Although affordable omics-based approaches have paved the way for quicker identification of putative biomarkers, validation of biomarkers is necessary for translation of discoveries into clinical application. Objective: Accordingly, in this study, we emphasize the potential of in silico approaches and have proposed and applied 3 novel sequential in silico pre-clinical validation steps to better identify the biomarkers that are truly desirable for clinical investment. Design: As protein biomarkers are becoming increasingly important in the clinic alongside other molecular biomarkers and lung cancer is the most common cause of cancer-related deaths, we used protein biomarkers for lung cancer as an illustrative example to apply our in silico pre-clinical validation approach. Methods: We collected the reported protein biomarkers for 3 cases (lung adenocarcinoma-LUAD, squamous cell carcinoma-LUSC, and unspecified lung cancer) and evaluated whether the protein biomarkers have cancer altering properties (i.e., act as tumor suppressors or oncoproteins and represent cancer hallmarks), are expressed in body fluids, and can be targeted by FDA-approved drugs. Results: We collected 3008 protein biomarkers for lung cancer, 1189 for LUAD, and 182 for LUSC. Of these protein biomarkers for lung cancer, LUAD, and LUSC, only 28, 25, and 6 protein biomarkers passed the 3 in silico pre-clinical validation steps examined, and of these, only 5 and 2 biomarkers were specific for lung cancer and LUAD, respectively. Conclusion: In this study, we applied our in silico pre-clinical validation approach the protein biomarkers for lung cancer cases. However, this approach can be applied and adapted to all cancer biomarkers. We believe that this approach will greatly facilitate the transition of cancer biomarkers into the clinical phase and offers great potential for future biomarker research. Plain Language Summary: Biomarkers, which are routinely used in clinics, allow better classification of patients according to their disease risk, prognosis, and/or response to treatment. Although affordable omics-based approaches have paved the way for quicker identification of putative biomarkers, validation of biomarkers is necessary for translation of discoveries into clinical application. This research article highlights the challenges of translating cancer biomarkers into clinical practice and summarizes feasible step toward "in silico pre-clinical validation" using the example of lung cancer types. Accordingly, protein biomarkers proposed for lung cancer are being investigated using the "in silico pre-clinical validation" approach to determine whether they have cancer altering properties (i.e., oncoprotein, tumor suppressor, and cancer hallmark), are expressed in body fluids (i.e., plasma/serum, saliva, urine, and bronchoalveolar lavage) and can be targeted with FDA-approved drugs. We believe that the step of in silico pre-clinical validation is the future of biomarker research for all professionals involved in clinical, biological, epidemiological, biostatistical and health research, and that it will greatly facilitate the transition of biomarkers to the clinical phase. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Lower COVID-19 Mortality in Patients with Type 2 Diabetes Mellitus Taking Dipeptidyl Peptidase-4 Inhibitors: Results from a Turkish Nationwide Study

Author

Emral, Rifat, Haymana, Cem, Demirci, Ibrahim, Tasci, Ilker, Sahin, Mustafa, Cakal, Erman, Ata, Naim, Unluturk, Ugur, Demir, Tevfik, Ertugrul, Derun, Sahin, Ibrahim, Atmaca, Aysegül, Celik, Osman, Caglayan, Murat, Arga, Kazim Yalcin, Dagdelen, Selcuk, Salman, Serpil, Satman, Ilhan, and Sonmez, Alper

Published
2021
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23. Correction to: Lower COVID-19 Mortality in Patients with Type 2 Diabetes Mellitus Taking Dipeptidyl Peptidase-4 Inhibitors: Results from a Turkish Nationwide Study

Author

Emral, Rifat, Haymana, Cem, Demirci, Ibrahim, Tasci, Ilker, Sahin, Mustafa, Cakal, Erman, Ata, Naim, Unluturk, Ugur, Demir, Tevfik, Ertugrul, Derun, Sahin, Ibrahim, Atmaca, Aysegül, Celik, Osman, Caglayan, Murat, Arga, Kazim Yalcin, Dagdelen, Selcuk, Salman, Serpil, Satman, Ilhan, and Sonmez, Alper

Published
2021
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26. Contributors

Author

Akhoon, Bashir Akhlaq, primary, Alarcón-Riquelme, Marta E., additional, Alberca, Lucas N., additional, Alice, Juan I., additional, Anuwongcharoen, Nuttapat, additional, Arga, Kazim Yalcin, additional, Belllera, Carolina L., additional, Berishvili, Vladimir P., additional, Bhardwaj, Anshu, additional, Bodiga, Vijaya Lakshmi, additional, Bodiga, Sreedhar, additional, Brylinski, Michal, additional, Carmona-Sáez, Pedro, additional, Chakraborti, Sohini, additional, Chaudhry, Vaishali, additional, Chen, Lixia, additional, Coumar, Mohane Selvaraj, additional, Toro-Domínguez, Daniel, additional, Dietis, Nikolas, additional, Douanne, Noelie, additional, Druzhilovskiy, Dmitry, additional, Eurídice Juárez-Mercado, K., additional, Fernández-Prada, Christopher, additional, Gautam, Pankaj, additional, Ghosh, Indira, additional, Mohan, C. Gopi, additional, Haider, Shozeb, additional, Hua, Li, additional, Iqbal, Jameel, additional, James, Nivya, additional, Jolly, Bani, additional, Kharkar, Prashant S., additional, Kim, Se-Min, additional, Kumar, Shivani, additional, Kumar, Suresh, additional, Kumar, Pawan, additional, Kurgan, Lukasz, additional, Lo, Yu-Chen, additional, López-López, Edgar, additional, Machhar, Janvhi S., additional, Manzoor, K., additional, Medina-Franco, José L., additional, Melge, Anu R., additional, Minadakis, George, additional, Minguez-Menendez, Aida, additional, Mitreva, Makedonka, additional, Monte-Neto, Rubens L., additional, Muneeswaran, Gurusamy, additional, Nagamani, Selvaraman, additional, Nair, Shantikumar V., additional, Nantasenamat, Chanin, additional, Sastry, G. Narahari, additional, Nargotra, Amit, additional, Nikitina, Anastasia A., additional, Orlov, Alexey A., additional, Osolodkin, Dmitry I., additional, Oulas, Anastasis, additional, Pal, Manoj Kumar, additional, Palyulin, Vladimir A., additional, Pandya, Ashma, additional, Passi, Anurag, additional, Pena, Joan, additional, Phanus-umporn, Chuleeporn, additional, Pires, Douglas E.V., additional, Poroikov, Vladimir, additional, Prieto-Martínez, Fernando D., additional, Radchenko, Eugene V., additional, Ramakrishnan, Gayatri, additional, Ramanathan, K., additional, Rosa, Bruce A., additional, Sahoo, Rosaleen, additional, Sahu, Niteshkumar U., additional, Sarica, Pemra Ozbek, additional, Sarvagalla, Sailu, additional, Savva, Kyriaki, additional, Sbaraglini, María L., additional, Schaduangrat, Nalini, additional, Serçinoğlu, Onur, additional, Shah, Chetan P., additional, Shanthi, V., additional, Sharma, Tina, additional, Sokratous, Kleitos, additional, Spyrou, George M., additional, Srinivasan, Narayanaswamy, additional, Sriwanichpoom, Nagaya, additional, Sun, Li, additional, Syed, Safiulla Basha, additional, Talevi, Alan, additional, Tiwari, Harshita, additional, Torres, Jorge Z., additional, Tunes, Luiza G., additional, Turanli, Beste, additional, Tyagi, Rahul, additional, Wang, Chen, additional, Wikberg, Jarl E.S., additional, Xia, Xuhua, additional, Yuen, Tony, additional, Zachariou, Margarita, additional, Zaidi, Neeha, additional, Zaidi, Samir, additional, Zaidi, Mone, additional, Zallone, Alberta, additional, and Zheng, Mengzhu, additional

Published
2019
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41. Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types

Author

Kori, Medi, Arga, Kazim Yalcin, Mardinoglu, Adil, Turanli, Beste, Kori, Medi, Arga, Kazim Yalcin, Mardinoglu, Adil, and Turanli, Beste

Abstract

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., QC 20220715

Published
2022
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44. Precision Diagnosis of Maturity-Onset Diabetes of the Young with Next-Generation Sequencing: Findings from the MODY-IST Study in Adult Patients

Author

Aydogan, Hulya Yilmaz, primary, Gul, Nurdan, additional, Demirci, Deniz Kanca, additional, Mutlu, Ummu, additional, Gulfidan, Gizem, additional, Arga, Kazim Yalcin, additional, Ozder, Aclan, additional, Camli, Ahmet Adil, additional, Tutuncu, Yildiz, additional, Ozturk, Oguz, additional, Cacina, Canan, additional, Darendeliler, Feyza, additional, Poyrazoglu, Sukran, additional, and Satman, Ilhan, additional

Published
2022
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47. Omics-Driven Biomarkers of Psoriasis: Recent Insights, Current Challenges, and Future Prospects

Author

Aydin, Busra, Arga, Kazim Yalcin, and Karadag, Ayse Serap

Subjects
psoriasis biomarkers, omics biomarkers, biomarker, Review, psoriasis, personalized medicine, omics, inflammatory skin diseases
Abstract

Advances in omics technologies have made it possible to unravel biomarkers from different biological levels. Intensive studies have been carried out to uncover the dysregulations in psoriasis and to identify molecular signatures associated with the pathogenesis of psoriasis. In this review, we presented an overview of the current status of the omics-driven biomarker research and emphasized the transcriptomic, epigenomic, proteomic, metabolomic, and glycomic signatures proposed as psoriasis biomarkers. Furthermore, insights on the limitations and future directions of the current biomarker discovery strategies were discussed, which will continue to comprehend broader visions of psoriasis research, diagnosis, and therapy especially in the context of personalized medicine.

Published
2020

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