Dataset Information

Ena-DATASET-MUG-11-09-2014-07:45:47:901-16 - samples

ABSTRACT: Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2

PROVIDER: EGAD00001001010 | EGA |

REPOSITORIES: EGA

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Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X.

Schulz Eduard E Klampfl Petra P Holzapfel Stefanie S Janecke Andreas R AR Ulz Peter P Renner Wilfried W Kashofer Karl K Nojima Satoshi S Leitner Anita A Zebisch Armin A Wölfler Albert A Hofer Sybille S Gerger Armin A Lax Sigurd S Beham-Schmid Christine C Steinke Verena V Heitzer Ellen E Geigl Jochen B JB Windpassinger Christian C Hoefler Gerald G Speicher Michael R MR Boland C Richard CR Kumanogoh Atsushi A Sill Heinz H

Nature communications 20141013

Familial colorectal cancer type X (FCCTX) is characterized by clinical features of hereditary non-polyposis colorectal cancer with a yet undefined genetic background. Here we identify the SEMA4A p.Val78Met germline mutation in an Austrian kindred with FCCTX, using an integrative genomics strategy. Compared with wild-type protein, SEMA4A(V78M) demonstrates significantly increased MAPK/Erk and PI3K/Akt signalling as well as cell cycle progression of SEMA4A-deficient HCT-116 colorectal cancer cells ...[more]

PMID: 25307848

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Project description:Purpose: The goals of this study are to determine the effect of microRNA-17 overexpression on 20,803 human genes in RASFs using Ion ProtonTM System platform. Human RASFs from two RA patients were transfected with pre-miR-17 or NC-pre-miR for 48 h and total RNA was prepared using miRNeasy kit (Qiagen). Total RNA integrity was checked using an Agilent Technologies 2100 Bio analyzer (Santa Clara, CA). 10 ng of high quality RNA was used to make cDNA for amplification with the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific). The cDNA was subjected to 12 cycles of amplification with panel primers and barcoded with adapters as recommended. Resulting sequencing libraries were quantified by qPCR using SYBR FAST master mix from KapaBiosystems (Wilmington, MA). Sets of eight libraries were balanced, pooled and sequencing beads produced on an Ion Chef. Sequencing was performed on an Ion P1 semi-conductor sequencing chip using an Ion Protonâ¢ System (ThermoFisher Scientific, Grand Island, NY). Data was collected and primary analysis performed using Torrent Suite software version 5.0.3. Reads were mapped to the panel and expression values determined. R Software version R-3.2.3 was used to generate heatmap. Among the panel of 20,803 genes, the expression of 15,067 genes as shown in the representative heat map was observed in pre-miR-17 and NC-pre-miR transfected RASFs. A total of 664 significantly modulated genes (301 upregulated and 363 downregulated) using Student âtâ test were further utilized for the IPA analysis. The result of IPA predicted the protein ubiquitin pathway as a major canonical pathway affected by the differentially regulated genes. Interestingly, IPA analysis generated an interactome that showed connectivity among various ubiquitin ligases, NF-ÔB family, AP-1/cJun, 20S and 26S proteasome system. Conclusion: Our results clearly shows the major pathways affected by miR-17 overexpression in RASFs were Protein ubiquitination related. mRNA profiles of pre-miR-17 and NC-pre-miR transfected RASFs were generated by AmpliSeq, in duplicate, using Ion Protonâ¢ System.

Dataset Information

Ena-DATASET-MUG-11-09-2014-07:45:47:901-16 - samples

Publications

Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X.

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