Sonderforschungsbereich 415:
"Specifity and Pathophysiology of Signal Transduction Pathways"

Project Z1: »Systematic expression analysis«

Changes on the cellular level can be monitored and described by the changes in the gene expression. The expression pattern of a cell can therefore provide important information about the actual status of a cell.

The microarray technology represents a tool, that enables the researcher to monitor a large number of expression levels in one experiment. In a first step, DNA fragments (representing transcripts) of known sequence are immobilized on a surface (e.g. glass). Each sequence is printed in a defined position. Then mRNA is extracted from the samples of interest and labelled with flourescent dyes. During the hybridization step, complementary sequences from the labelled sample bind to their corresponding, immobilized targets on the array. The resulting signal intensity, located in a particular position of the array represents the relative amount of the associated transcript in the original sample.

In collaboration with all the SFB participants we selected genes which are of relevance to four different topics:

1. Apoptosis array (408 genes) - PCR product based glass array
2. Differentiation and regeneration array (526 genes) - PCR product based glass array
3. Inflammation and infection array (418 genes) - PCR product based glass array
4. Mouse array (403 genes) - oligonucleotide based glass array

All samples are labelled with Cy3 and/or Cy5 and the target sequences are spotted on telecem glass slides.

The Z1 project holds responsibility for quality control, quality maintenance and experimental workflow. Additionally the largest part of bioinformatic analysis is covered by the Z1 project. As part of the bioinformatic analysis, new normalization techiques had to be developed which was carried out in collaboration with the bioinformatics group of the first department of medicine, Kiel.

1. Continuing ongoing systematic expression analysis in collaboration with the projects A2, A3, A10, A14 (now A15), B2 and C8 with the special emphasis on verification of the expression patterns in larger cohorts.
2. The projects A4, A11, A12, A13, B5, B6, B8, B9, C6 and C7 will start according to the schedule in the next funding period with systematic expression analysis.
3. Application of alternative, commerical microarrays with special emphasis on whole genome arrays.
4. Providing access to the high throughput real time PCR verificaiton platform, which has been established by the Z1 project within the last 2 years.

Original papers

Chalaris A, Adam N, Sina C, Rosenstiel P, Lehmann J, Schirmacher P, Hartmann D, Cichy J, Gavrilova O, Schreiber S, Jostock T, Matthews V, Häsler R, Becker C, Neurath MF, Reiß K, Saftig P, Scheller J, Rose-John S. (2010) Critical Role of the Disintegrin Metalloprotease ADAM17 for Intestinal Inflammation and Regeneration in Mice.

J Exp Med 207:1617-1624

Franke A, Balschun T, Sina C, Ellinghaus D, Häsler R, Mayr G, Albrecht M, Wittig M, Buchert E, Nikolaus S, Gieger C, Wichmann HE, Sventoraityte J, Kupcinskas L, Onnie CM, Gazouli M, Anagnou NP, Strachan D, McArdle WL, Mathew CG, Rutgeerts P, Vermeire S, Vatn MH and the IBSEN study group, Krawczak M, Rosenstiel P, Karlsen TH, Schreiber S. (2010) Genome-wide association study for ulcerative colitis demonstrates novel associations with IL17REL and 7q22.

Nat Genet 42:292-294

Kuenzel S, Till A, Winkler M, Haesler R, Lipinski S, Jung S, Grötzinger J, Fickenscher H, Schreiber S, Rosenstiel P. (2010) The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses.

J Immunol 184:1990-2000

Kuenzel S, Till A, Winkler M, Haesler R, Lipinski S, Jung S, Grötzinger J, Fickenscher H, Schreiber S, Rosenstiel P. (2010) The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses.

J Immunol 184:1990-2000

Kuenzel S, Till A, Winkler M, Haesler R, Lipinski S, Jung S, Grotzinger J, Fickenscher H, Schreiber S, Rosenstiel P. (2010) The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses.

J Immunol 184:1990-2000

Häsler R, Begun A, Freitag-Wolf S, Kerick M, Mah N, Zvirbliene A, Spehlmann ME, von Wurmb-Schwark N, Kupcinskas L, Rosenstiel P, Schreiber S. (2009) Genetic control of global gene expression levels in the intestinal mucosa: a human twin study.

Physiol Genomics 38:73-79

Herrmann J, Rubin D, Häsler R, Helwig U, Pfeuffer M, Auinger A, Laue C, Winkler P, Bell D, Schreiber S, Schrezenmeir J. (2009) Isomer-specific effects of CLA on gene expression in human adipose tissue depending on PPARgamma2 P12A polymorphism.

Lipids Health Dis 8:35

Nebel A, Flachsbart F, Till A, Caliebe A, Blanché H, Arlt A, Häsler R, Jacobs G, Kleindorp R, Franke A, Shen B, Nikolaus S, Krawczak M, Rosenstiel P, Schreiber S. (2009) A functional EXO1 promoter variant is associated with prolonged life expectancy in centenarians.

Mech Ageing Dev130:691-9

Sina C, Gavrilova O, Förster M, Till, A, Derer S, Hildebrand F, Rabe B, Scheller J, Chalaris A, Scheller J, Rehmann A, Franke A, Ott S, Häsler R, Nikolaus S, Fölsch UR, Rose-John S, Jiang H-P, Li J, Schreiber S, Rosenstiel P. (2009) G-protein coupled receptor 43 (GPR43) is essential for neutrophil recruitment during intestinal inflammation.

J Immunol 183:7514-7522

Sina C, Gavrilova O, Foerster M, Till A, Derer S, Hildebrand F, Raabe B, Chalaris A, Scheller J, Rehmann A, Franke A, Ott S, Haesler R, Nikolaus S, Folsch UR, Rose-John S, Jiang HP, Li J, Schreiber S, Rosenstiel P. (2009) G protein-coupled receptor 43 is essential for neutrophil recruitment during intestinal inflammation.

J Immunol 183:7514-7522

Sina C, Gavrilova O, Foerster M, Till A, Derer S, Hildebrand F, Raabe B, Chalaris A, Scheller J, Rehmann A, Franke A, Ott S, Häsler R, Nikolaus S, Folsch UR, Rose-John S, Jiang HP, Li J, Schreiber S, Rosenstiel P. (2009) G protein-coupled receptor 43 is essential for neutrophil recruitment during intestinal inflammation.

J Immunol 183:7514-7522

Ufer M, Häsler R, Jacobs G, Haenisch S, Lächelt S, Faltraco F, Sina C, Rosenstiel P, Nikolaus S, Schreiber S, Cascorbi I. (2009) Decreased sigmoidal ABCB1 (P-glycoprotein) expression in ulcerative colitis is associated with disease activity.

Pharmacogenomics 10:1941-53

Ufer M, Häsler R, Jacobs G, Haenisch S, Lächelt S, Faltraco F, Sina C, Rosenstiel P, Nikolaus S, Schreiber S, Cascorbi I. (2009) Decreased sigmoidal ABCB1 (P-glycoprotein) expression in ulcerative colitis is associated with disease activity.

Pharmacogenomics 10:1941-53

Ufer M, Mosyagin I, Muhle H, Jacobsen T, Haenisch S, Häsler R, Faltraco F, Remmler C, von Spiczak S, Kroemer HK, Runge U, Boor R, Stephani U, Cascorbi I. (2009) Non-response to antiepileptic pharmacotherapy is associated with the ABCC2 -24C>T polymorphism in young and adult patients with epilepsy.

Pharmacogenet Genomics 19:353-62

Rosenstiel P, Derer S, Till A, Häsler R, Eberstein H, Bewig B, Nikolaus S, Nebel A, Schreiber S. (2008) Systematic expression profiling of innate immune genes defines a complex pattern of immunosenescence in peripheral and intestinal leukocytes.

Genes Immun 9:103-114

Rosenstiel P, Derer S, Till A, Häsler R, Eberstein H, Bewig B, Nikolaus S, Nebel A, Schreiber S. (2008) Systematic expression profiling of innate immune genes defines a complex pattern of immunosenescence in peripheral and intestinal leukocytes.

Genes Immun 9:103-114

Schulze HA, Häsler R, Mah N, Lu T, Nikolaus S, Costello CM, Schreiber S. (2008) From model cell line to in vivo gene expression: disease-related intestinal gene expression in IBD.

Genes Immun 9: 240-248

Schulze HA, Häsler R, Mah N, Lu T, Nikolaus S, Costello CM, Schreiber S. (2008) From model cell line to in vivo gene expression: disease-related intestinal gene expression in IBD.

Genes Immun 9:240-248

Ufer M, Dilger K, Leschhorn L, Daufresne L, Mosyagin I, Rosenstiel P, Häsler R, Kuehbacher T, Nikolaus S, Schreiber S, Cascorbi I. (2008) Influence of CYP3A4, CYP3A5, and ABCB1 Genotype and Expression on Budesonide Pharmacokinetics: A Possible Role of Intestinal CYP3A4 Expression.

Clin Pharmacol Ther 84:43-6

Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Gunther S, Prescott NJ, Onnie CM, Hasler R, Sipos B, Folsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.

Nat Genet 39:207-211

Gottschlich S, Ambrosch P, Cordes C, Luhmann B, Görögh T, Wurmb-Schwark N, Schreiber S, Häsler R. (2006) Gene expression profiling of head and neck squamous cell carcinoma using cDNA microarrays

Int J Oncol 29:605-613

Muerköster SS, Lust J, Arlt A, Häsler R, Witt M, Sebens T, Schreiber S, Fölsch UR, Schäfer H. (2006) Acquired chemoresistance in pancreatic carcinoma cells: induced secretion of IL-1beta and NO lead to inactivation of caspases.

Oncogene 25:3973-81

Schroeder T, Meier-Stiegen F, Schwanbeck R, Eilken H, Nishikawa S, Häsler R, Schreiber S, Bornkamm GW, Nishikawa SI, Just U. (2006) Activated Notch1 alters differentiation of embryonic stem cells into mesodermal cell lineages at multiple stages of development

Mech Dev 123:570-579

Sebens Müerköster S, Lust E, Arlt A, Witt M, Häsler R, Sebens T, Schreiber S, Fölsch UR, Schäfer H. (2006) Acquired chemoresistance in pancreatic carcinoma cells - Induced secretion of IL1ß and NO lead to inactivation of caspases

Oncogene 25:3973-3981

Costello CM, Mah N, Hasler R, Rosenstiel P, Waetzig GH, Hahn A, Lu T, Gurbuz Y, Nikolaus S, Albrecht M, Hampe J, Lucius R, Kloppel G, Eickhoff H, Lehrach H, Lengauer T, Schreiber S. (2005) Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays

PLoS Med 2:e199

Lu T, Costello CM, Croucher PJ, Häsler R, Deuschl G, Schreiber S. (2005) Can Zipf's law be adapted to normalize microarrays

BMC Bioinformatics 6:37

Mah N, Thelin A, Lu T, Nikolaus S, Kuhbacher T, Gurbuz Y, Eickhoff H, Klöppel G, Lehrach H, Mellgard B, Costello CM, Schreiber S. (2005) A comparison of oligonucleotide and cDNA-based microarray systems

Physiological Genomics 16:361-370

Valentonyte R, Hampe J, Huse K, Rosenstiel P, Albrecht M, Stenzel A, Nagy M, Gaede KI, Franke A, Haesler R, Koch A, Lengauer T, Seegert D, Reiling N, Ehlers S, Schwinger E, Platzer M, Krawczak M, Muller-Quernheim J, Schurmann M, Schreiber S. (2005) Sarcoidosis is associated with a truncating splice site mutation in BTNL2

Nat Genet 37:357-364

Weichart D, Gobom J, Klopfleisch S, Häsler R, Gustavsson N, Billmann S, Lehrach H, Seegert D, Schreiber S, Rosenstiel P. (2005) Analysis of NOD2-mediated proteome response to muramyl-dipeptide in HEK293 cells.

J Biol Chem 28:28