功能基因组学与肝脏疾病研究

Screening and identification of target genes differentially expressed in HepG2 cells treated with arsenic trioxide by suppression subtractive hybridization technique

AIM: To clone and identify human genes differentially expressed in human hepatocarcinoma HepG2 cells treated with arsenic trioxide by constructing a subtractive cDNA library with suppression subtractive hybridization (SSH) technique, and to elucidate the molecular mechanism of arsenic trioxide in the regulation of liver cells.

METHODS: The mRNA was isolated from HepG2 cells treated with arsenic trioxide and PBS, respectively, and then cDNA was synthesized. After digestion of restriction enzyme RsaI, small sizes cDNA were obtained. Then the tester cDNA was subdivided into two portions and each was ligated with a different cDNA adaptor. After the tester cDNA was hybridized with driver cDNA (twice) and underwent nested polymerase chain reaction (PCR) (twice), the DNA fragment was subcloned into T/A plasmid vectors to establish the subtractive cDNA library. Amplification of the library was performed in E. coli strain JM109. The amplified cDNA was sequenced and analyzed in GenBank with BLAST search after colony PCR.

RESULTS: The subtractive cDNA library of genes differentially expressed in HepG2 cells treated with arsenic trioxide was constructed successfully. The amplified library contained 109 positive clones. Colony PCR showed that these clones all contained 200-1 000 bp inserts. Thirty-six clones were analyzed by sequencing and bioinformatics. The results showed there were 15 coding sequences with known function and 6 novel ones with unknown function.

CONCLUSION: A subtractive cDNA library of genes differentially expressed in HepG2 cells treated with arsenic trioxide was constructed successfully using SSH technique.

Comparison of target genes transactivated by different spliced transcripts of human NS5ATP2

AIM: To identify and analyze target genes regulated by different spliced transcripts of human NS5ATP2 by microarray technique.

METHODS: The coding sequences for the two differently spliced transcripts of human NS5ATP2, NS5ATP2 (615) and NS5ATP2, were cloned into eukaryotic expression vector pcDNA3.1 to yield pcDNA3.1-NS5ATP2 (615) and pcDNA3.1-NS5ATP2 (216) constructs, which were then transfected into HepG2 cells. The differentially expressed genes in the cells transfected with the two differently spliced variants were analyzed and compared by DNA microarray.

RESULTS: Forty-three genes were up-regulated by both NS5ATP2 (615) and NS5ATP2 (216), and 13 genes were down-regulated by both NS5ATP2 (615) and NS5ATP2 (216). Meanwhile, 3 genes were found to be up-regulated by NS5ATP2 (615), but down-regulated by NS5ATP2 (216). No genes were down-regulated by NS5ATP2 (615) while up-regulated by NS5ATP2 (216). Many genes were trans-regulated by NS5ATP2 (615) or NS5ATP2 (216) independently.

CONCLUSION: Different spliced transcripts of human NS5ATP2 may commonly or independently regulate target genes. They even exhibit opposite regulatory effects upon some target genes.

N/A

N/A

Identification and analysis of rat homologous gene to human HBV pre-S1 protein-binding protein

AIM: To identify and analyze rat homologous gene to human hepatitis B virus (HBV) pre-S1-binding protein (PS1BP) coding gene.

METHODS: The human PS1BP was screened and identified from a hepatocyte expressive cDNA library by phage display technique with purified recombinant pre-S1 protein of HBV as the solidified matrix. The nucleotide sequence database GenBank, established by National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institute of Health (NIH), was searched for rat cDNA sequence homologous to human PS1BP cDNA by BLASTn tools online. A homologous cDNA sequence was identified as the rat PS1BP cDNA. The similarity and identity of rat PS1BP cDNA and amino acid (aa) sequences to human and mouse PS1BP genes were compared. The potential functional domains were predicted by online analysis tools.

RESULTS: The human PS1BP cDNA was identified by phage display technique. The rat PS1BP cDNA was identified by bioinformatics methods. The rat PS1BP cDNA consisted of 1 455 nt, and encoded a protein of 484 aa. The identity of rat PS1BP protein to human and mouse PS1BP proteins was 80.79% (391/484) and 92.98% (450/484), respectively. In the rat PS1BP protein sequence, several potential modification domains were identified.

CONCLUSION: Rat PS1BP cDNA and protein primary sequences are identified and analyzed.

Screening and identification of genes trans-regulated by HBV pre-S2 protein with cDNA microarray

AIM: To understand the target genes up-regulated or down-regulated by HBV pre-S2 protein, we compared the differentially expressed genes between the hepatoblastoma cell line HepG2 transfected by pcDNA3.1(-) and pcDNA3.1(-)-preS2, respectively with cDNA microarray technique.

METHODS: The HBV pre-S2 coding DNA fragment was amplified with polymerase chain reaction (PCR) technique by using G376-7 plasmid containing the full length of HBV genome as the template. The expressive vector of pcDNA3.1-preS2 was constructed by routine molecular biological methods. The HepG2 cells were transfected by pcDNA3.1(-) and pcDNA3.1(-)-preS2, respectively, using FuGENE6 transfection reagent. The total RNA was isolated and reversely transcribed. The cDNAs were subjected for microarray screening with 1 152 cDNA probes.

RESULTS: The expressive vector was constructed and confirmed by restriction enzyme digestion and DNA sequencing analysis. High quality mRNA and cDNA were prepared and successful microarray screening conducted. From the scanning results, it was found 42 genes were up-regulated and 36 genes down-regulated by pre-S2 protein of HBV.

CONCLUSION: HBV pre-S2 protein is a transactivator. The expression of pre-S2 protein affects the expression spectrum of HBV infected hepatocyte.

Identification and analysis of murine and rat homologous gene to human NS5ATP4 by bioinformatics method

AIM: To identify and analyze murine and rat NS5ATP4 cDNA sequences homologous to human NS5ATP4 cDNA sequence.

METHODS: The human NS5ATP4 cDNA was identified by combination of molecular biology and bioinformatics methods. The GenBank was searched for NS5ATP4 homologous cDNA sequences from mouse and rat. The identity and similarity were compared between human mouse and rat NS5ATP4 cDNA sequences.

RESULTS: The murine and rat NS5ATP4 cDNAs were consisted of 762 nucleotides (nt) and 756 nt, respectively. They encoded a protein of 253 amino acid residues (aa) and 251 aa, respectively. The similarity of murine and rat NS5ATP4 to human homologue was 90.29% and 84.25%, respectively, and the identity of murine and rat NS5ATP4 to human homologue was 95.65% and 86.96%, respectively.

CONCLUSION: The murine and rat NS5ATP4 cDNAs are identified.

N/A

N/A