Additional Supporting Information may be found in the online version of this article.

HEP_24682_sm_SuppFig1.tif891KFigure S1. Down-regulation of a subset of 25 cellular miRNAs in HCC patient samples. miRNA expression was determined by miRNA Taqman microfluidic array in 3 healthy liver (HL) and 10 HCC samples (etiology: alcohol). Ct values were normalized with control mammalian U6 snRNA (dCt), average of HCC was normalized to average of HL (ddCt), and fold change in expression between HL and HCC was calculated according to the 2-Δ& Delta;Ct method of Livak and Schmittgen (29). 79 miRNAs were significantly down-regulated; a subset of 25 is presented here.
HEP_24682_sm_SuppFig2.tif52KFigure S2. Schematic representation of ABCA1 3'UTR (middle part), the fragments used in Luc-ABCA1-5' and Luc-ABCA1-3' (upper part) and the fragments used in the composite Luc-ABCA1 (lower part).
HEP_24682_sm_SuppFig3.tif884KFig. S3. Analysis of the correlation between ABC genes expression and the expression of validated miRNAs, in 10 or 19 patient samples (miRNA profiling in all 19 patient samples was done only for miR-135b, miR-199a-3p, miR-199a, miR-199b and miR-296). Each point represents one patient sample and shows the corresponding gene and miRNA relative expression (fold change between HCC and adjacent healthy liver (AHL)).
HEP_24682_sm_SuppTables.doc255KTable S1. miRNA target predictions in ABC genes. 51 miRNA targets were predicted in the 3'UTR of 6 out of 15 ABC genes using TargetScan and PicTar algorithms. miRNAs targets are summarized in the table, where x represent a single target sequence in the 3' untranslated region (3'UTR); xx, two targets sequences in the 3'UTR; xxx, three targets sequences. Detailed prediction analysis is presented in Table S2. miR-203-mediated regulation of ABCE1 was verified (27). Table S2. miRNA targets were predicted in the 3' untranslated region (3'UTR) of the ABC genes, using algorithms TargetScan, PicTar, and additional manual screening. Targets were identified in the 3'UTR of 6 ABC genes. miRNAs selected for further validation are bold. Table S3. Oligonucleotides used in this study. Genome sequences around the primary miRNA (pri-miRNA) in the PCR primers are in bold. Table S4. Sequences of the mutated ABC 3' untranslated region (3'UTR) that were synthesized and cloned into psiCheck-2 vector to construct mutated Luc-ABC reporters and composite ABCA1 3'UTR. Table S5. ABC gene profiling in 19 paired HCC patient samples. Expression of 15 ABC genes was determined by custom-made ABC Taqman microfluidic array in 19 paired adjacent healthy liver (AHL) and HCC samples. Ct values were normalized with control 18S rRNA (dCt), each sample was normalized with the average dCt of the AHL group (ddCt), and fold change in expression (FC) was calculated according to the 2-& Delta;& Delta;Ct method of Livak and Schmittgen (29). Up-regulations (FC≥1.5) are marked in green and down-regulation (FC≤0.5) are marked in red). Table S6. Conservation among species of dysregulated miRNAs. miRNA conservation was determined using the UCSC Genome Browser. An x marks the miRNA conservation in the stated specie.

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