E-GEOD-46622 - High-throughput sequencing of matched colorectal normal, tumor and metastasis tissues and proof-of principal bioinformatics modeling of therapeutic consequences of miRNA applications

Status
Released on 18 September 2013, last updated on 3 May 2014
Organism
Homo sapiens
Samples (36)
Protocols (2)
Description
MiRNAs are discussed as diagnostic and therapeutic molecules. However, effective miRNA drug treatments with miRNAs are so far hampered by the complexity of the miRNA networks. To identify potential miRNA drugs in colorectal cancer, we profiled miRNA and mRNA expression in matching normal, tumor and metastasis tissues of eight patients by Illumina sequencing. We identified miRNA-1 as top candidate differentially expressed in tumor and metastasis. Furthermore, miRNA-1 was de-regulated in 16 additional tumor entities underscoring its central role in tumor pathogenesis. Functional analyses showed an additive effect of miRNA-1 with camptothecin treatment. We used a systems-biology simulation of cellular cancer models implemented in PyBios to investigate miRNA-1 function and assessed the effects of depletion as well as overexpression in terms of miRNA-1 as a potential treatment option. In this system miRNA-1 treatment reverted the disease phenotype with different effectiveness among the patients. Scoring the gene expression changes obtained through mRNA-Seq from the same patients we show that the combination of deep sequencing and systems biological modeling can help to identify patient-specific responses to miRNA treatments. We present this data as guideline for future pre-clinical assessments of new and personalized therapeutic options. Examination of miRNA expression values by Illumina sequencing of matched benign, tumor and metastasis tissues of 8 colorectal cancer patients. For 4 of these patients all tissues have been resequenced to obtain mRNA expression values.
Experiment types
RNA-seq of coding RNA, RNA-seq of non coding RNA 
Contacts
Michal Ruth Schweiger <mschweig@molgen.mpg.de>, Alexander Kuehn, Alice C McHardy, Andrea Wunderlich, Anja Nowka, Axel Fischer, Bernd Timmermann, Christian Barmeyer, Christian Viertler, Christina Roehr, Christina Tusche, Christoph Wierling, Dmitriy Drichel, Hans Lehrach, Karl Kashofer, Kurt Zatloukal, Martin Kerick, Michal R Schweiger, Stefan T Boerno, Sylvia Krobitsch, Thomas Meinel, Tim Becker
Citation
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. R�hr C, Kerick M, Fischer A, K�hn A, Kashofer K, Timmermann B, Daskalaki A, Meinel T, Drichel D, B�rno ST, Nowka A, Krobitsch S, McHardy AC, Kratsch C, Becker T, Wunderlich A, Barmeyer C, Viertler C, Zatloukal K, Wierling C, Lehrach H, Schweiger MR. , Europe PMC 23874421
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-46622.idf.txt
Sample and data relationshipE-GEOD-46622.sdrf.txt
Processed data (1)E-GEOD-46622.processed.1.zip
Links