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

FilenameFormatSizeDescription
HEP_24495_sm_SuppInfoFig1.tif3381KSupporting Information Figure 1. Gene ontology enrichment of 362 DEGs within the regions of 1,241 somatic CNAs.
HEP_24495_sm_SuppInfoFig2.tif2026KSupporting Information Figure 2. q-PCR analyses of mRNA levels of differentially expressed genes within the aberrant regions in 47 paired HCC and adjacent non-tumor tissues. A. q-PCR analyses of expression levels of 20 candidate genes selected for further functional assessments, including 13 upregulated genes (DDEF1, SHC1, HAX1, RAD21, MPZL1, YWHAZ, PEA15, ILF2, SNRPE, C1ORF2, BOP1, HEY1 and DUSP12) and 7 downregulated genes (SERPINA5, GNAO1, MT1G, PER1, C8ORF4, SLC25A4 and TRIM35). p < 0.05 was considered significant. B. q-PCR analyses of expression levels of eight differentially expressed genes within eight new CNAs, including four upregulated genes in four regions of copy number gain (COL4A1 in 13q33.3-34, CLN3 in 16p12.1-11.2, BMI1 in 10p12.31-12.1 and GNAZ in 22q11.22) and four downregulated genes in four regions of copy number loss (FOS in 14q23.2-31.1, HGFAC in 4p16.2-16.1, CDH19 in 18q22.1 and SERPINA6 in 14q31.1-32.13). p < 0.05 was considered significant.
HEP_24495_sm_SuppInfoFig3.tif5633KSupporting Information Figure 3. q-PCR analyses of mRNA levels of 20 candidate genes in eight liver cancer cell lines q-PCR analyses of relative expression levels of 20 candidate genes (DDEF1, SHC1, HAX1, RAD21, MPZL1, YWHAZ, PEA15, ILF2, SNRPE, C1ORF2, BOP1, HEY1, DUSP12, SERPINA5, GNAO1, MT1G, PER1, C8ORF4, SLC25A4 and TRIM35) in eight liver cancer cell lines, including Hep3B, PLC/PRF/5, HUH-7, HepG2, SK-Hep-1, SMMC-7721, MHCC-97L and HCCLM3.
HEP_24495_sm_SuppInfoFig4.tif1766KSupporting Information Figure 4. q-PCR analyses of overexpression of the 20 candidate genes in SMMC-7721 and HUH-7 cells A and B. q-PCR analyses of overexpression of TRIM35, HEY1 and SNRPE in SMMC-7721 and HUH-7 cells, respectively. C. q-PCR analyses of overexpression of 17 candidate genes (DDEF1, SHC1, HAX1, RAD21, MPZL1, YWHAZ, PEA15, ILF2, C1ORF2, BOP1, DUSP12, SERPINA5, GNAO1, MT1G, PER1, C8ORF4 and SLC25A4) in HUH-7 cells.
HEP_24495_sm_SuppInfoFig5.tif982KSupporting Information Figure 5. q-PCR analyses of siRNA knockdown of TRIM35, HEY1 and SNRPE in HepG2 cells.
HEP_24495_sm_SuppInfoFig6.tif1010KSupporting Information Figure 6. Detection and quantitation of TRIM35 methylation in 31 paired HCC and adjacent paracancer tissues by real-time methylation-specific PCR. The methylation status of CpG islands within TRIM35 promoter was examined by quantitative real-time methylation-specific PCR on 31 out of 58 paired HCC and matched paracancer tissues. Totally, 18 out of 31 HCC tissues were methylation-positive, whereas 9 out 31 non-tumor tissues were methylation-positive. Noticeably, among the 18 methylation-positive HCC cases, the methylation of TRIM35 promoter was also observed in 7 corresponding non-tumor tissues, however, the methylation levels in 6 HCC tissues was higher than those in the corresponding non-tumor tissues. Additionally, among the remaining 11 methylation-positive HCC tissues, 3 also harbored copy number loss of the 14q32.13 loci, which targets the TRIM35 gene. In summary, the frequency of hypermethylation was approximately 45.2% (14/31) in HCCs, which accounted for the downregulation of TRIM35 mRNA and protein level in HCC tissues in addition to that caused by genomic loss of 14q32.13 loci (17.2%).
HEP_24495_sm_SuppInfoFig7.tif2438KSupporting Information Figure 7. SERPINA5 inhibited HCC cell migration, but not cell growth. A. Representative result of CCK-8 assays for the effects of SERPINA5 gene on the in vitro proliferation of SMMC-7721 and Huh-7 cells by lentivirus-mediated overexpression. B. The effects of the SERPINA5 gene on the growth abilities of SMMC-7721 cells in xenograft models of nude mice (n=6) as determined by tumor weight. C. The effects of the SERPINA5 gene on the migration abilities of SMMC-7721 and Huh-7 cells by Trans-well migration assays. All the results are shown as the mean ± s.e.m. **, p<0.01; ***, p<0.001.
HEP_24495_sm_SuppInfo.doc650KSupporting Information

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