Projects
Name
Brachyury Expression in Atypical Teratoid Rhabdoid Tumors
University
Turkey (TurkMSIC) - Hacettepe University, Ankara
Domain
Pathology
Departement
Hacettepe University,Department of Pathology, Sihiyye Campus, Sihiyye, 06230, Ankara
Head
Kemal KOSE MEHMETOGLU
Tutor
Figen SOYLEMEZOGLU
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 Yes Yes No No No
Type of Research Project
- Clinical Project with Laboratory work
What is the background of the project?
Atypical teratoid rhabdoid tumor (ATRT), a highly aggressive brain tumor of childhood, is composed of primitive appearing rhabdoid cells with characteristic Integrase Interactor Protein 1 (INI1) loss. Poorly differentiated chordoma (PDC) is a recently described entity classically located at base of skull-clivus and spinal cord, and also lacks INI1 loss but shows brachyury expression which is regarded as a distinction between these two entities. Brachyury expression in classical ATRT of cerebrum is not well known. The pathology laboratories are capable of a number of functions, such as: PCR (Polymerase Chain Reaction), real-time PCR, Western/Northern Blot, and laser microdissection. In addition, The Turkish Society of Pathology, founded in 1966, organizes annual meetings in order to further knowledge of its respective field, and to strengthen the connections between other branches of science. It also aims to prevent malpractice of its respective field. Hacettepe University Faculty of Medicine, Department of Pathology hosts a Cytopathology and a Pediatric Pathology unit, as well as having routine paraffin monitoring, specific histochemistry, immunofluorescence / immunohistochemistry, molecular pathology and research laboratories, macroscopy and microscopy rooms.
What is the aim of the project?
To find the proportion of brachyury expression in classical ATRT, and comparing the expression with PDC to determine differences.
What techniques and methods are used?
Tissue Microarray Formation: Tissue microarrays are composite paraffin blocks constructed by extracting cylindrical tissue core “biopsies” from different paraffin donor blocks and re-embedding these into a single recipient (microarray) block at defined array coordinates. At first, the donor blocks (invariably stored paraffin blocks) are retrieved and sectioned to produce standard microscopic slides that are stained with hematoxylin and eosin. An experienced pathologist examines the slides to mark the area of interest, which is commonly an area of cancer, after which the samples can be arrayed. A tissue microarray instrument is used to acquire a tissue core from the donor block. This core is then placed in an empty paraffin block—the recipient block. The current Beecher Instruments arraying device is designed to produce sample circular spots that are 0.6 mm in diameter at a spacing of 0.7-0.8 mm. The surface area of each sample is 0.282 mm2, or in pathologists' terms, about the size of 2-3 high power fields. The number of spots on a single slide is variable depending on the array design; the current comfortable maximum with the 0.6 mm needle is about 600 spots per standard glass microscope slide. The core is placed at a specifically assigned coordinate (X-Y guide), which is accurately recorded, typically on a spreadsheet, such as Microsoft Excel. The sampling process can then be repeated many times from different donor blocks until hundreds, or even thousands, of cores are placed into one recipient block, producing the final tissue microarray block. Using a microtome, 5 μm sections are cut from the still sue microarray blocks to generate tissue microarray slides for molecular and immunohistochemical analyses. Immunohistochemistry: The tissue will be stained with peroxidase, which forms a conjugate with the antibodies. This produces a colored product. Light Microscopy.
What is the role of the student?
- The student will mainly observe
- If the project includes “lab work”
- the student will take active part in the practical aspect of the project
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
● Allocation of paraffin blocks from archive. ● Finding the relevant areas in tissue sections for microarray formation. ● Formation of tissue microarray blocks. ● Macroscopical examination ● Microscopical examination ● Evaluation of brachyury and INI1 immunohistochemistry ● Learning about the principles of immunohistochemistry ● Evaluation between PDC and ARTR tissues. ● Staying in line with lab procedures/protocols
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
The subject will be taught on how to perform Tissue Microarray Formation, and immunohistochemical staining once per week by tutor Prof.Dr.Kemal KOSE MEHMETOGLU depending on the availability of the teacher: -Explaining a tissue microarray instrument is used to acquire a tissue core from the donor block. This core is then placed in an empty paraffin block—the recipient block - Explaining ımmunohistochemistry: The tissue willbe stained with peroxidase, which forms a conjugate with the antibodies. This produces a colored product.
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
- No specific outcome is expected
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
No specific skills are required. Student must have completed 2nd year of medical studies.
Are there any legal limitations in the student’s involvement
No
Hours
6
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
Articles
- Poorly differentiated chordoma: review of 53 cases. Yeter et al. APMIS 2019: 127; 607-615 doi: 10.1111 Atypical teratoid rhabdoid tumors-current concepts; advances in biology; and potential future therapies Frühwald et al Neuro Oncol 2016: 18; 764-78 doi: 10.1093/neuonc/nov264 SMARCB1 deficient tumors of childhood: A practical guide. Pawel et al. Pediatr Dev Pathol. 2018: 21; 6-28