Genomics

Dataset Information

43

Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture


ABSTRACT: We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p<0.01) between CC-CR and CC; there were 141 transcripts upregulated and 220 transcripts downregulated in CC-CR compared to CC. Small RNA-Seq detected 7 miRNAs upregulated and 24 miRNAs downregulated in CC-CR cells compared to CC cells (fold change>2, FDR<0.01). Differential expression analysis revealed several novel candidates that may contribute to cetuximab resistance. The whole-transcriptome profilings using cetuximab resistance model from 3D culture provide novel candidates for cetuximab resistance and further functional studies might open the door to a novel understanding of how non-mutational mechanisms mediate cetuximab resistance. Overall design: mRNA and small-RNA profiles of cetuximab sensitive CC and resistant CC-CR from 3D culture were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 sequencer.

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Robert Coffey  

PROVIDER: GSE82236 | GEO | 2017-08-30

SECONDARY ACCESSION(S): PRJNA324412

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE82236_RNAseq_counts.txt.gz Txt
GSE82236_miRNA_counts.txt.gz Txt
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Publications


De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of kno  ...[more]

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