Microsatellite instability at U2AF-binding polypyrimidic tract sites perturbs alternative splicing during colorectal cancer initiation

Microsatellite instability (MSI) due to mismatch repair deficiency (dMMR) is common in colorectal cancer (CRC). To date, MSI in CRC has been found to be associated with somatic coding events, but the noncoding pathophysiological impact of this mode of genomic instability is yet poorly understood. Here we performed an extensive analysis of coding and noncoding MSI events at the different steps of colorectal tumorigenesis using whole exome and searched for associated splicing events via RNA sequencing at the bulk-tumor. To do these analysis we have sequenced 3 datasets, the first one of whole exome from bulk-tumor and paired healthy tissue. A second one of RNA-seq of bulk-tumor with a part of them being from the same samples as the ones in the previous dataset. The third one of whole exome from precancerous samples mainly obtained from lynch patients.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006666	This dataset contain 45 pairs of colorectal tumor and adjacent normal tissue. Four of them are from a previous study EGAS00001002477. For each sample a BAM was generated by aligning to GRCh37. Those colorectal cancer all have the MSI phenotype.	Illumina HiSeq 2000	90
EGAD00001006667	This dataset contain 133 pairs of colorectal tumor and adjacent normal tissue. For each sample paired RNA-seq fastq were generated using an Illuma Myseq-2000. Those colorectal cancer comprise 101 MSI and 32 MSS tumors.	Illumina HiSeq 2000	266
EGAD50000000644	Raw sequencing data of WES that were obtained from precancerous samples as adenoma and MMR-deficient crypts and paired healthy tissue from MSI CRC patients of which 10 are diagnosed with lynch syndrome and 3 had sporadic cancer. These data were analyzed in order to evaluate microsatellite instability though tumorigenesis and associated to splicing deregulation in MSI tumors RNA.	Illumina NovaSeq 6000	36

Publications	Citations
Microsatellite instability at U2AF-binding polypyrimidic tract sites perturbs alternative splicing during colorectal cancer initiation. Jonchère V, Montémont H, Le Scanf E, Siret A, Letourneur Q, Tubacher E, Battail C, Fall A, Labreche K, Renault V, Ratovomanana T, Buhard O, Jolly A, Le Rouzic P, Feys C, Despras E, Zouali H, Nicolle R, Cervera P, Svrcek M, Bourgoin P, Blanché H, Boland A, Lefèvre J, Parc Y, Touat M, Bielle F, Arzur D, Cueff G, Le Jossic-Corcos C, Quéré G, Dujardin G, Blondel M, Le Maréchal C, Cohen R, André T, Coulet F, de la Grange P, de Reyniès A, Fléjou JF, Renaud F, Alentorn A, Corcos L, Deleuze JF, Collura A, Duval A. Genome Biol 25: 2024 210	1

Publications

Citations

Microsatellite instability at U2AF-binding polypyrimidic tract sites perturbs alternative splicing during colorectal cancer initiation.
Jonchère V, Montémont H, Le Scanf E, Siret A, Letourneur Q, Tubacher E, Battail C, Fall A, Labreche K, Renault V, Ratovomanana T, Buhard O, Jolly A, Le Rouzic P, Feys C, Despras E, Zouali H, Nicolle R, Cervera P, Svrcek M, Bourgoin P, Blanché H, Boland A, Lefèvre J, Parc Y, Touat M, Bielle F, Arzur D, Cueff G, Le Jossic-Corcos C, Quéré G, Dujardin G, Blondel M, Le Maréchal C, Cohen R, André T, Coulet F, de la Grange P, de Reyniès A, Fléjou JF, Renaud F, Alentorn A, Corcos L, Deleuze JF, Collura A, Duval A. Genome Biol 25: 2024 210