title: Integrated microRNA, mRNA, and protein expression profiling reveals microRNA regulatory networks in rat kidney treated with a carcinogenic dose of aristolochic acid.
abstract: BACKGROUND
  Aristolochic Acid (AA), a natural component of Aristolochia plants that is found in a variety of herbal remedies and health supplements, is classified as a Group 1 carcinogen by the International Agency for Research on Cancer. Given that microRNAs (miRNAs) are involved in cancer initiation and progression and their role remains unknown in AA-induced carcinogenesis, we examined genome-wide AA-induced dysregulation of miRNAs as well as the regulation of miRNAs on their target gene expression in rat kidney.
  
  
  RESULTS
  We treated rats with 10 mg/kg AA and vehicle control for 12 weeks and eight kidney samples (4 for the treatment and 4 for the control) were used for examining miRNA and mRNA expression by deep sequencing, and protein expression by proteomics. AA treatment resulted in significant differential expression of miRNAs, mRNAs and proteins as measured by both principal component analysis (PCA) and hierarchical clustering analysis (HCA). Specially, 63 miRNAs (adjusted p value < 0.05 and fold change > 1.5), 6,794 mRNAs (adjusted p value < 0.05 and fold change > 2.0), and 800 proteins (fold change > 2.0) were significantly altered by AA treatment. The expression of 6 selected miRNAs was validated by quantitative real-time PCR analysis. Ingenuity Pathways Analysis (IPA) showed that cancer is the top network and disease associated with those dysregulated miRNAs. To further investigate the influence of miRNAs on kidney mRNA and protein expression, we combined proteomic and transcriptomic data in conjunction with miRNA target selection as confirmed and reported in miRTarBase. In addition to translational repression and transcriptional destabilization, we also found that miRNAs and their target genes were expressed in the same direction at levels of transcription (169) or translation (227). Furthermore, we identified that up-regulation of 13 oncogenic miRNAs was associated with translational activation of 45 out of 54 cancer-related targets.
  
  
  CONCLUSIONS
  Our findings suggest that dysregulated miRNA expression plays an important role in AA-induced carcinogenesis in rat kidney, and that the integrated approach of multiple profiling provides a new insight into a post-transcriptional regulation of miRNAs on their target repression and activation in a genome-wide scale.
authors.affiliation: Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University, Dalian, 116044, China. zhiguangli@dlmedu.edu.cn.
authors.forename: Zhiguang
authors.initials: Z
authors.lastname: Li
authors.affiliation: Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. qincharles1@gmail.com.
authors.forename: Taichun
authors.initials: T
authors.lastname: Qin
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. kejian.wang.bio@gmail.com.
authors.forename: Kejian
authors.initials: K
authors.lastname: Wang
authors.affiliation: Genetics Department, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain. mlhack@gmail.com.
authors.forename: Michael
authors.initials: M
authors.lastname: Hackenberg
authors.affiliation: Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. jian.yan@fda.hhs.gov.
authors.forename: Jian
authors.initials: J
authors.lastname: Yan
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. yuan.gao@fda.hhs.gov.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. LiRong.Yu@fda.hhs.gov.
authors.forename: Li-Rong
authors.initials: LR
authors.lastname: Yu
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. leming.shi@gmail.com.|Current address: School of Pharmacy, Fudan University, Shanghai, 201203, China. leming.shi@gmail.com.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. Zhenqiang.Su@fda.hhs.gov.
authors.forename: Zhenqiang
authors.initials: Z
authors.lastname: Su
authors.affiliation: Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA. tao.chen@fda.hhs.gov.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
mesh_terms: D000818:Animals; D034341:Aristolochic Acids / Q000633:toxicity*; D002273:Carcinogens / Q000633:toxicity*; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D053263:Gene Regulatory Networks / Q000187:drug effects; D059014:High-Throughput Nucleotide Sequencing; D007668:Kidney / Q000187:drug effects* / Q000378:metabolism; D007680:Kidney Neoplasms / Q000209:etiology / Q000235:genetics* / Q000378:metabolism*; D008297:Male; D035683:MicroRNAs / Q000032:analysis; D008969:Molecular Sequence Data; D040901:Proteomics; D012333:RNA, Messenger / Q000032:analysis; D012334:RNA, Neoplasm / Q000032:analysis*; D051381:Rats; D017423:Sequence Analysis, RNA
chemical_list: D034341:Aristolochic Acids; D002273:Carcinogens; D035683:MicroRNAs; D012333:RNA, Messenger; D012334:RNA, Neoplasm; C000228:aristolochic acid I