Abstract A14: The transcriptomic landscape of the two emblematic colorectal cancer cell lines HCT116 and HT29

Abstract

Abstract Colorectal cancer (CRC) is the third leading cause of malignant mortality worldwide, accounting for more than 13% of all cancer death. CRC harbors several alterations, mainly, two major classes of these instability were described: 1/microsatellite instability (MSI) caused by the inactivation and loss of expression of the mismatch repair genes (MMR), and 2/chromosome instability or microsatellite stable (MSS). CRC Cell lines are invaluable biomedical research tools to study these alterations. Two emblematic cell lines for CRC were extensively used, HT29 for MSS and HCT116 for MSI. Short and long reads, high coverage whole transcriptome sequencing of these two cell lines and two normal cell lines, enable us to establish the signaling pathways altered in these two cancer cell lines. Method: Total RNA were extracted from four cell lines HT29, HCT116, CR1780 and CRL18 using RNeasy Mini Kit (Qiagen). mRNA libraries were generated using TruSeq Stranded mRNA Library Prep Kit (Illumina), and high-throughput sequencing were performed using Illumina Systems. Pair-end reads of 100bp and 300bp were generated by Hiseq and Miseq, respectively. All reads were filtered for high-quality reads (≥Q30, adapters trimming and broken pair-reads removing). Reads alignment and genes profiling analysis were done with CLCbio software. Genes upregulated and downregulated with p-value <0.05, in cancer cell lines versus normal cell lines and between the two cancer cell lines were analyzed by Ingenuity Pathways Analysis (IPA). Results: The transcriptome analysis reveals 11,564 different splice variants are differentially expressed in both cancer cell lines HT29 and HCT116, when compared to the two normal cell lines (p-value <0.05). Among which, 9041 transcripts are upregulated and 2523 downregulated. The comparison between HT29 and HCT116 reveals only 333 splice variants differentially expressed. The canonical signaling pathways analysis demonstrates extensive molecular heterogeneity in cancer cell lines. in which, two major pathways clearly appear, mTOR signaling pathway (mTORsp) and estrogen receptor signaling pathway (ERsp). Half or more the number of molecules, which constitute these two pathways, has altered transcription expression, 96 genes among 194 molecules of mTORsp, and 66 genes among 127 molecules of ERsp. Interestingly, when comparing cancer cell lines with each other, 47 genes among 194 of mTORsp have altered expression and no gene from ERsp was found. Conclusion: Our finding established the signaling pathways altered in HT29 and HCT116 and shows the importance of mTOR and estrogen receptor signaling pathways in these two cancer cell lines. Citation Format: Hicham Mansour, Noureddine BOUAROUROU, Jean-Pierre Roperch, Faouzi Habib, Mourad Said. The transcriptomic landscape of the two emblematic colorectal cancer cell lines HCT116 and HT29. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A14.