Projects
Name
Elucidation of mystery side of truncated KIT (tyrosine kinase-cKIT; Cluster of Differentiation 117 or mast/stem cell growth factor receptor) protein variant in prostate cancer
University
Turkey (TurkMSIC) - Ordu University, Ordu
Domain
Biology
Departement
Department of Medical Biology, Bucak District, Nefsi Bucak Street, Ordu University Research-Training Hospital, No: 94/1, Post Code: 52200, Ordu/Altınordu
Head
Asst. Prof. Dr. Sercan ERGUN
Tutor
Asst. Prof. Dr. Sercan ERGUN
Languages
Turkish, English
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No Yes Yes No No No No No
Type of Research Project
- Basic science
What is the background of the project?
Prostate cancer (PCa) is the most common cancer type in men. New and more precise biomarkers are needed for the diagnosis and response to treatment of PCa. Through an alternative promoter, a truncated c-KIT protein (tr-KIT) lacking the extracellular and transmembrane region is created. Upregulation of tr-KIT with PCa progression makes it a pharmacological target. Therefore, tr-KIT expression control is gaining importance. Imatinib is a tyrosine kinase inhibitor blocking full-length c-KIT but has no effect on tr-KIT; this explains ineffectiveness of this drug in PCa. Furthermore, we think it is important to use serum exosome specimens to evaluate the molecular mechanism of tr-KIT in patient with PCa and control groups.
What is the aim of the project?
What is the aim of the project? (Highly specific: purpose?) We aim to find answers to following questions via proposed project: Is it possible to suppress both tr-KIT and tr-KIT activated oncogenic pathway by inhibition of transcription factors controlling tr-KIT expression? Can anti-proliferative activity of Imatinib on PCa be increased by inhibition of tr-KIT specific transcription factors? How are tr-KIT and tr-KIT-mediated pathway elements, and tr-KIT transcription factors affected in serum exosome samples of PCa and Benign Prostatic Hyperplasia (BPH) patients, and healthy controls? Is there an association between tr-KIT-dependent factors and clinical parameters of patients with PCa and BPH? Proposed project maintains its original value through all these questions and experimental approaches performed to answer these questions.
What techniques and methods are used?
What techniques and methods are used? Mention the steps/stages in this project. (Provide examples and avoid abbreviations; which tools will be used in general in this project?) In this project proposed, transcriptomic data of LNCaP (tr-KIT-expressing PCa cells), PC3 (tr-KIT non-expressing PCa Type) and RWPE-1 (normal prostate epithelial cell) cell lines were compared with respect to gene expression levels of potential tr-KIT transcription factors (YY1, c-MYB, IL8, NFYA ve TCF3), and YY1 and NFYA were defined as the most probable tr-KIT specific transcription factors. After silencing tr-KIT transcription factors, YY1 and NFYA, by siRNAs (small interference RNA- a class of double-stranded RNA, 20-25 base pairs in length and operating within the RNA interference pathway, It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation.) transfection methods in cell lines, the effects of them on expressions of tr-KIT and activated pathway elements, and proliferation of LNCaP cells will be investigated via mainly by RT-PCR (Real-Time Polymerase Chain Reaction; it is a method by which the amount of the PCR (Polymerase chain reaction make several copies of a specific DNA segment.) product can be determined, in real-time, and is very useful for investigating gene expression.) methods. Anti-proliferative efficacies of Imatinib and Imatinib + siRNA applications on LNCaP cell line will be compared by MTT (a colorimetric assay for measuring cell metabolic activity) method. Moreover, serum exosome samples of PCa, BPH and healthy individuals will be compared through tr-KIT pathway via Real-Time PCR experiments
What is the role of the student?
- The student will mainly observe
What are the tasks expected to be accomplished by the student?
What techniques and methods are used? Mention the steps/stages in this project. (Provide examples and avoid abbreviations; which tools will be used in general in this project?) In this project proposed, transcriptomic data of LNCaP (tr-KIT-expressing PCa cells), PC3 (tr-KIT non-expressing PCa Type) and RWPE-1 (normal prostate epithelial cell) cell lines were compared with respect to gene expression levels of potential tr-KIT transcription factors (YY1, c-MYB, IL8, NFYA ve TCF3), and YY1 and NFYA were defined as the most probable tr-KIT specific transcription factors. After silencing tr-KIT transcription factors, YY1 and NFYA, by siRNAs (small interference RNA- a class of double-stranded RNA, 20-25 base pairs in length and operating within the RNA interference pathway, It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation.) transfection methods in cell lines, the effects of them on expressions of tr-KIT and activated pathway elements, and proliferation of LNCaP cells will be investigated via mainly by RT-PCR (Real-Time Polymerase Chain Reaction; it is a method by which the amount of the PCR (Polymerase chain reaction make several copies of a specific DNA segment.) product can be determined, in real-time, and is very useful for investigating gene expression.) methods. Anti-proliferative efficacies of Imatinib and Imatinib + siRNA applications on LNCaP cell line will be compared by MTT (a colorimetric assay for measuring cell metabolic activity) method. Moreover, serum exosome samples of PCa, BPH and healthy individuals will be compared through tr-KIT pathway via Real-Time PCR experiments
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
No.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a scientific report
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
No specific skills are required.
Are there any legal limitations in the student’s involvement
No
Hours
6
Type of students accepted
This project accepts:
- Medical students
- Pre-Medical students from the American-British system
Articles
- - Ergun; S.; Altay; D. U.; Gunes; S.; Buyukalpelli; R.; Karahan; S. C.; Tomak; L.; & Abur; U. (2019). Tr-KIT/c-KIT ratio in renal cell carcinoma. Molecular biology reports; 1-8.