Unknown,Transcriptomics,Genomics,Proteomics

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Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells

ABSTRACT: Antrodia cinnamomea (Ac), a traditional medicine and an endemic fungus in Taiwan, has been used in cancer research. Recent research has revealed decreased cell proliferation after treatment of Ac on tumor. In this study, we profiled the 2 hours and 4 hours genome-wide miRNA and mRNA transcriptome by next-generation sequencing techniques to report the early apoptotic effect on Ac fruiting body extract treated human hepatocarcinoma cells, SK-HEP-1, instead of prolonged treatment. Results showed that miRNAs were globally downregulated during the first 2-4 hours in, and solely in, AcFBE-treated SK cells. The inhibition of miRNAs imposed no discrimination against any particular miRNA species, but oncogenic miR-21, miR-191 and two oncogenic clusters miR-17-92 and miR-106b-25 were among the most significantly inhibited miRNAs. In addition to miRNA expression, mRNA transcriptome data indicated the association of apoptosis mechanism with AcFBE treatment. Western blotting indicated a decrease in key proteins Drosha and Dicer required for miRNA biogenesis, and an increase of XRN2 involved in miRNA degradation. Our results suggest that miRNAs appeared to be the prime targets of Ac in disrupting multiple miRNA regulatory pathways and global disruption of miRNA transcriptome resulting in activation of extrinsic and intrinsic (mitochondrial) pathways. Human liver SK-Hep-1 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 and SOLiD 5500xl to obtain miRNA profiles; mRNA profiles also were profiled by SOLID 3. Mouse liver BNL CL.2 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 to obtain miRNA profiles.

ORGANISM(S): Mus musculus

SUBMITTER: mike thang

PROVIDER: E-GEOD-48327 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Twenty-four triple-negative breast cancer and 14 adjacent normal tissues were collected from breast cancer patients during surgeries at National Taiwan University Hospital (NTUH, Taipei, Taiwan). All triple-negative breast cancer samples were invasive ductal carcinomas (IDC) and were negative in immunohistochemical statuses of ER, PR, and HER2 receptors, as confirmed by professional pathologists. Treatment procedure of all patients followed the National Comprehensive Cancer Network (NCCN) guideline. All samples were neoadjuvant-free and were collected before systemic chemotherapy treatments. Written informed consent was obtained from all patients who participated in this study. Using human tissues for research in this study was approved by the institutional review board at NTUH. A novel set of 25-miRNA signature identified in this study was able to effectively distinguish between triple-negative breast cancer and adjacent normal tissues. Moreover, we documented the first evidence of seven polycistronic miRNA clusters preferentially harboring deregulated miRNA genes in triple-negative breast cancer. In the present study, a panel of 24 triple-negative breast cancer and 14 adjacent normal tissue samples were examined for the presence of deregulated miRNA genes using the high-throughput sequencing technology. Total RNA was extracted from the triple-negative breast cancer and adjacent normal samples for preparation of small RNA libraries. Each small RNA library was constructed from total RNA of each sample using the SOLiD Total RNA-Seq Kit (Applied Biosystems, Foster City, CA, USA). Upon completion of polymerase chain reaction (PCR) amplification, small RNA libraries were purified using the SOLiD Library Micro Column Purification Kit (Applied Biosystems) and hybridized to the template beads using the SOLiD EZ bead system (Applied Biosystems). The template beads were amplified and deposited onto subtract for ligation sequencing by SOLiD 4 System (Applied Biosystems).

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Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells

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