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Functional Genomics
 
April 17 - 21
Coordinators: Paulo Santos and Stephen Bustin

Lecturers:
 
 
Jo Vandesompele (MD, PhD)
 
Center for Medical Genetics Ghent (CMGG); Ghent University Hospital, Medical Research Building (MRB), 2nd floor, room 120.055 De Pintelaan 185, B-9000 Ghent, Belgium. Phone: +32 9 240 5187; Fax: +32 9 240 6549.
 
Katja Kotsch (MD, PhD)
 
Institute of Medical Immunology, Universitätsmedizin Charité, Schumannstrasse 20/21, D-10117 Berlin, Germany. Phone +49 30 450524357 Fax +49 30 450524907.
 
 
Molecular Biology Unit, Microbiology Service, Hospital Geral de Santo António, R. D. Manuel II, 4099-001 Porto.
Coordinators:
 
 
 
Center for Histocompatiblity of the Centre, Coimbra
 
 
Barts and the London Queen Mary’s School of Medicine and Dentistry, University of London
Objectives:
This course will focus on Laser Capture Microdissection (LCM) and quantitative gene expression using real-time PCR (qPCR) analysis applied to oncobiology, clinical transplantation and microbiology. The course aimed at discussing the impact of different strategies for nucleic acid extraction, purification, reverse transcription and quantification on molecular analysis in human disease and experimental models. Special attention will be dedicated to application of bioinformatics tools for data analysis in biomedical sciences.
COURSE SCHEDULE:
 
Lectures (two per morning)
1.
Laser Capture Microdissection: basic principles and biomedical applications
2.
Real-time PCR: principles and quantification strategies
3.
Template preparation for real-time PCR analysis: problems and solutions
4.
Accurate gene expression profiling facing the issues of normalization and efficiency
5.
Tools for normalisation and data analysis
6.
Gene expression profile in colon cancer
7.
Gene expression profile in clinical transplantation
8.
Real-time PCR in microbiology
 
Experimental sessions (afternoons)
 
From tissue samples to relative gene expression profile and absolute quantification
 
(practical examples in oncobiology, clinical transplantation and microbiology)
 
Seminar (Friday 16:00)
 
Combining Laser Capture Microdissection and real-time PCR analysis for biomedical research
Publications of invited speakers
 
Jenkins PJ, Khalaf S, Ogunkolade W, McCarthy K, David T, Hands RE, Davies D, Bustin SA. Differential expression of IGF-binding protein-3 in normal and malignant colon and its influence on apoptosis. Endocr Relat Cancer. 2005 Dec;12(4):891-901.
 
Bustin SA, Mueller R. Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci (Lond). 2005 Oct;109(4):365-79.
 
Bustin SA. Real-time, fluorescence-based quantitative PCR: a snapshot of current procedures and preferences. Expert Rev Mol Diagn. 2005 Jul;5(4):493-8.
 
Bustin SA, Dorudi S. Gene expression profiling for molecular staging and prognosis prediction in colorectal cancer. Expert Rev Mol Diagn. 2004 Sep;4(5):599-607.
 
Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech. 2004 Sep;15(3):155-66.
 
Lacha J, Hribova P, Kotsch K, Brabcova I, Bartosova K, Volk HD, Vitko S. Effect of cytokines and chemokines (TGF-beta, TNF-alpha, IL-6, IL-10, MCP-1, RANTES) gene polymorphisms in kidney recipients on posttransplantation outcome: influence of donor-recipient match. Transplant Proc. 2005 Mar;37(2):764-6.
 
Hribova P, Kotsch K, Brabcova I, Vitko S, Volk HD, Lacha J. Cytokines and chemokine gene expression in human kidney transplantation. Transplant Proc. 2005 Mar;37(2):760-3.
 
Kuecuek O, Mantouvalou L, Klemz R, Kotsch K, Volk HD, Jonas S, Wesslau C, Tullius S, Neuhaus P, Pratschke J. Significant reduction of proinflammatory cytokines by treatment of the brain-dead donor. Transplant Proc. 2005 Jan-Feb;37(1):387-8.
 
Martins PN, Mashreghi MF, Reutzel-Selke A, Neuhaus P, Volk HD, Tullius SG, Kotsch K. Quantification of donor-derived DNA in serum: a new approach of acute rejection diagnosis in a rat kidney transplantation model. Transplant Proc. 2005 Jan-Feb;37(1):87-8.
 
Kotsch K, Mashreghi MF, Bold G, Tretow P, Beyer J, Matz M, Hoerstrup J, Pratschke J, Ding R, Suthanthiran M, Volk HD, Reinke P. Enhanced granulysin mRNA expression in urinary sediment in early and delayed acute renal allograft rejection. Transplantation. 2004 Jun 27;77(12):1866-75.
 
Gantois I, Vandesompele J, Speleman F, Reyniers E, D´Hooge R, Severijnen LA, Willemsen R, Tassone F, Kooy RF. Expression profiling suggests underexpression of the GABA(A) receptor subunit delta in the fragile X knockout mouse model. Neurobiol Dis. 2005 Sep 29; [Epub ahead of print]
 
De Preter K, Vandesompele J, Menten B, Carr P, Fiegler H, Edsjo A, Carter NP, Yigit N, Waelput W, Van Roy N, Bader S, Pahlman S, Speleman F. Positional and functional mapping of a neuroblastoma differentiation gene on
chromosome 11. BMC Genomics. 2005 Jul 6;6:97.
 
Vandesompele J, Baudis M, De Preter K, Van Roy N, Ambros P, Bown N, Brinkschmidt C, Christiansen H, Combaret V, Lastowska M, Nicholson J, O´Meara A, Plantaz D, Stallings R, Brichard B, Van den Broecke C, De Bie S, De Paepe A, Laureys G, Speleman F. Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. J Clin Oncol. 2005 Apr 1;23(10):2280-99.
 
De Preter K, Vandesompele J, Heimann P, Kockx MM, Van Gele M, Hoebeeck J, De Smet E, Demarche M, Laureys G, Van Roy N, De Paepe A, Speleman F. Application of laser capture microdissection in genetic analysis of neuroblastoma and neuroblastoma precursor cells. Cancer Lett. 2003 Jul 18;197(1-2):53-61. Review.
 
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002 Jun 18;3(7):RESEARCH0034. Epub 2002 Jun 18.
 
Vandenbroucke II, Vandesompele J, Paepe AD, Messiaen L. Quantification of splice variants using real-time PCR. Nucleic Acids Res. 2001 Jul 1;29(13):E68-8.

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