A 40 h module consisting of lectures, guest lectures, research seminars, group work (including the use of Mir@nt@n-based informatics) and practical course
Objective:
To describe microRNA and transcription factor (TF) interaction as a key regulatory system in the determination of cell phenotype through regulation of marker gene expression. To describe how microRNA signatures of cell phenotypes are determinant for normal organ functioning and pathophysiology.
Lectures by Jan Oxholm Gordeladze:
1. Introduction to the course: MicroRNAs, synthesis and function (1 lecture)
2. MicroRNAs and transcription factors in stem cell renewal and differentiation, strategies of how to search for phenotype-specific microRNA signatures, microRNAs in exosomes (cell-cell microRNA communication), introduction to practical courses (5 lectures)
Guest lectures:
1. Joel Glover - Stem cells, self renewal and differentiation potential
2. Enikö Sonkoly - MicroRNAs as disease markers: focus on the immune system and inflammation
3. Jörg Haier – MicroRNAs and cancer: predictors and modifiers of chemo- and radiotherapy in different tumour types
Lunch seminars:
These will be seminars featuring results obtained during the practical laboratory work sessions and bioinformatics sessions within a given scientific context (performed by the PhD-students)
Schedule: Wednesday-Friday, 12.00-13.00
Practical laboratory course and bioinformatics analyses:
The objective is to provide practical information on how microRNA and transcription factors interact in differentiating stem cells, how to use a microRNA species as a disease marker. Furthermore, the different databases (including Mir@nt@n)) will be used as part of the strategy to identify important microRNA vs transcription factor networks. Lastly, the students will get some hands on experience related to the analyses of microRNA and transcription factor expression as well as traditional staining techniques identifying osteoblasts, chondrocytes and adipocytes differentiated from mesenchymal stem cells or fat tissue derived stem cells.
Outline of lab-work:
Part 1:
• Cell staining techniques, light microscopy, assessment of percentage of marker-positive surfaces (mineralization, proteoglycans, fat droplets) using predifferentiated osteoblasts, chondrocytes and adipocytes from 14 day cultures
Part 2:
• Isolation of total RNA from 14 day cultures of differentiated osteoblasts, chondrocytes, and adipocytes. Q-PCR analyses of transcription factors and selected microRNAs
Practical group work (non-lab):
Two modules:
• Module 1: Work on an assigned practical problem encompassing trimmed (small) transcriptomes and microRNA micro-arrays to arrive at a putative network linking microRNAs and transcription factors together. Analysis of hierarchical structures and identifying putative important players in the development of cell phenotypes. Group presentation of findings and discussion. To be performed over 3 days.
• Module 2: Journal club - to analyze and present orally one relevant publication chosen from an assigned list using the paper to shed light on experimental findings. The PhD-students will work in groups of 2-4 (depending on how many groups).
Location: The course is held in Domus Medica and Domus Odontologica, Sognsvannsveien 9
Tentative course schedule:
Monday 31st January:
09.00-11.00 - Seminar Room GA02 A1.1004 (Domus Odontologica)
• Stem cells, self renewal and differentiation potential (Lecturer 1- J. Glover, Institute of Physiology, Inst. Of Basic Medical Science, University of Oslo, Norway)
• Introduction to course: MicroRNA, synthesis and function (Jan Oxholm Gordeladze, Dept. of Biochemistry, Inst. of Basic medical Science, University of Oslo, Norway = JOG)
11.00-12.00 - Seminar Room GA02 A1.1004 (Domus Odontologica)
• MicroRNA and transcription factors in stem cell renewal (JOG)
12.00-13.00
• Lunch break (no seminar)
13.00-17.00 - Seminar Room GA01 1128 (Domus Medica)
• Literature studies (literature package), assigned reading
Tuesday 1st February:
09.00-11.00 - Auditorium GA02 A1.1001 (Domus Odontologica)
• MicroRNAs as disease markers: focus on the immune system and inflammation (Lecturer 2 – Dr. E. Sonkoly, Molecular Dermatology Research Group, Unit of Dermatology and Venerology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden)
• How to study microRNAs in stem cell differentiation: Strategies, general approach (JOG)
11.00-12.00 - Seminar Room GA01 1128 (Domus Medica)
• Prepare for lab work, cell staining techniques (intro by JOG)
12.00-13.00
• Lunch break (no seminar)
13.00-19.00 - Laboratory GA01 1123 and Seminar Room GA01 1128 (Domus Medica)
• Cell staining, light microscopy, qualitative assessment of percentage of marker-positive cells/cell surfaces (MSCs differentiated to osteoblasts, chondrocytes and adipocytes)
• Literature studies (literature package), assigned tasks
Wednesday 2nd February:
09.00-11.00 - GA01 2031 Lille Auditorium (Domus Medica)
• How to search for phenotype-specific microRNA signatures (JOG): specific approach
11.00-13.00 - Seminar Room GA01 1128 (Domus Medica)
• Seminar 1 (during lunch) on cell staining and literature studies (PhD students)
13.00-17.00 - GA01 2031 Lille Auditorium and Seminar Room GA01 1128 (Domus Medica)
• Use of bioinformatics to create regulatory networks linking microRNAs, transcription factors and phenotypic marker genes (Lecture by JOG and practical work)
Thursday 3rd February:
09.00-11.00 - Auditorium GA02 A1.1001 (Domus Odontologica)
• MicroRNAs and cancer: predictors and modifiers of chemo- and radiotherapy in different tumour types (Lecturer 3 – Dr. J. Haier, Comprehensive Cancer Center, Muenster, University Hospital Muenster, University of Muenster, Germany)
• Cell-to-cell communication through microRNAs in exosomes: Implications for cell engineering (JOG)
11.00-13.00 - Seminar Room GA01 1128 (Domus Medica)
• Seminar 2 (during lunch) on regulatory networks (PhD students)
13.00-19.00 - Laboratory GA01 1123 and Seminar Room GA01 1128 (Domus Medica)
• Practical course: Analyze transcription factors and selected microRNA species in samples of total RNA from differentiated mesenchymal stem cells (MSCs) and adipose stem cells (ASCs)
• Literature studies (literature package), assigned reading
Friday 4th February:
09.00-12.00 - Seminar Room GA01 1128 (Domus Medica)
• Practical course (cont.): Complete Q-PCR analyses: Calculations and preparing for data presentation and discussion (PhD students)
12.00-14.00 - Seminar Room GA01 1128 (Domus Medica)
• Seminar 3 (during “late” lunch) Data presentation and discussion: emphasis on phenotype acquisition – selections of stem cell sources for cell engineering (PhD students)
14.00-15.00 - Seminar Room GA01 1128 (Domus Medica)
• Evaluation of course
15.00-17.00 - Seminar Room GA01 1128 (Domus Medica)
• Written exam (multiple choice)
Grading (pass or fail): Will be based on seminar performances, demonstration of practical skills, an essay with title/subject chosen by the participant (home exam), and the results obtained in the “multiple choice” session. Home exam to be finalized 14 days after completion of the course – should be submitted to Jan O. Gordeladze via e-mail no later than February 18th, 2011, 5.00 pm.