Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE

Dong, Hui; Ge, Xijin; Yan, Shaofeng; Chen, Lin-Lei; Kong, Yalin; Zhang, Hongyi; Man, Xiao-hua; Tang, Liang; Yuan, Hong; Wang, Hongyang; Zhao, Guoping; Jin, Weihua

doi:10.1186/1755-8794-2-5

Cited by 27 publications

(27 citation statements)

References 36 publications

(34 reference statements)

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“…Highly up-regulated (up to 44-fold change) in the Pak1-KO MEFs are Pdlim1 gene PDZ - LIM domain 1 and Sgce gene (sarcoglycan-epsilon) which encodes the epsilon member of the sarcoglycan family . Both PDLIM1 and SGCE are known to play role in human cancers and cytoskeleton signaling [17] [18] [19] [20]. SGCE is a member of transmembrane proteins, which acts as a link between actin cytoskeleton and the extra cellular matrix and is also implicated in neuronal disorder such as myoclonus-dystonia syndrome .…”

Section: Resultsmentioning

confidence: 99%

Identification of Novel Gene Targets and Functions of p21-Activated Kinase 1 during DNA Damage by Gene Expression Profiling

et al. 2013

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P21-activated kinase 1 (PAK1), a serine/threonine protein kinase, modulates many cellular processes by phosphorylating its downstream substrates. In addition to its role in the cytoplasm, PAK1 also affects gene transcription due to its nuclear localization and association with chromatin. It is now recognized that PAK1 kinase activity and its nuclear translocation are rapidly stimulated by ionizing radiation (IR), and that PAK1 activation is a component of the DNA damage response. Owing to the role of PAK1 in the cell survival, its association with the chromatin, and now, stimulation by ionizing radiation, we hypothesize that PAK1 may be contributing to modulation of genes with roles in cellular processes that might be important in the DNA damage response. The purpose of this study was to identify new PAK1 targets in response to ionizing radiation with putative role in the DNA damage response. We examined the effect of IR on the gene expression patterns in the murine embryonic fibroblasts with or without Pak1 using microarray technology. Differentially expressed transcripts were identified using Gene Spring GX 10.0.2. Pathway, network, functional analyses and gene family classification were carried out using Kyoto Encyclopedia of Genes and Genomes (KEGG), Ingenuity Pathway, Gene Ontology and PANTHER respectively. Selective targets of PAK1 were validated by RT-qPCR. For the first time, we provide a genome-wide analysis of PAK1 and identify its targets with potential roles in the DNA damage response. Gene Ontology analysis identified genes in the IR-stimulated cells that were involved in cell cycle arrest and cell death. Pathway analysis revealed p53 pathway being most influenced by IR responsive, PAK1 targets. Gene family of transcription factors was over represented and gene networks involved in DNA replication, repair and cellular signaling were identified. In brief, this study identifies novel PAK1 dependent IR responsive genes which reveal new aspects of PAK1 biology.

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Section: Resultsmentioning

confidence: 99%

Identification of Novel Gene Targets and Functions of p21-Activated Kinase 1 during DNA Damage by Gene Expression Profiling

et al. 2013

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“…Although there are no known published reports of porcine SGCE isoforms, nine possible isoforms have been predicted by genome annotation in the mouse, and four in humans [46]. Recently, it has been reported that SGCE is upregulated in human hepatocellular carcinoma [55], suggesting that SGCE plays a role in hepatocyte proliferation. Thus, it is plausible that maternal expression of the usually silent allele, leading to a relative increase in SGCE levels, is a compensatory mechanism present at a developmental time of very rapid liver growth.…”

Section: Identification Of Tissue-specific Imprintingmentioning

confidence: 99%

Characterization of Conserved and Nonconserved Imprinted Genes in Swine1

Bischoff

Tsai

Hardison

et al. 2009

Biology of Reproduction

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To increase our understanding of imprinted genes in swine, we carried out a comprehensive analysis of this gene family using two complementary approaches: expression and phenotypic profiling of parthenogenetic fetuses, and analysis of imprinting by pyrosequencing. The parthenote placenta and fetus were smaller than those of controls but had no obvious morphological differences at Day 28 of gestation. By Day 30, however, the parthenote placentas had decreased chorioallantoic folding, decreased chorionic ruggae, and reduction of fetal-maternal interface surface in comparison with stage-matched control fetuses. Using Affymetrix Porcine GeneChip microarrays and/or semiquantitative PCR, brain, fibroblast, liver, and placenta of Day 30 fetuses were profiled, and 25 imprinted genes were identified as differentially expressed in at least one of the four tissue types: AMPD3, CDKN1C, COPG2, DHCR7, DIRAS3, IGF2 (isoform specific), IGF2AS, IGF2R, MEG3, MEST, NAP1L5, NDN, NNAT, OSBPL1A, PEG3, APEG3, PEG10, PLAGL1, PON2, PPP1R9A, SGCE, SLC38A4, SNORD107, SNRPN, and TFPI2. For DIRAS3, PLAGL1, SGCE, and SLC38A4, tissue-specific differences were detected. In addition, we examined the imprinting status of candidate genes by quantitative allelic pyrosequencing. Samples were collected from Day 30 pregnancies generated from reciprocal crosses of Meishan and White Composite breeds, and single-nucleotide polymorphisms were identified in candidate genes. Imprinting was confirmed for DIRAS3, DLK1, H19, IGF2AS, NNAT, MEST, PEG10, PHLDA2, PLAGL1, SGCE, and SNORD107. We also found no evidence of imprinting in ASB4, ASCL2, CD81, COMMD1, DCN, DLX5, and H13. Combined, these results represent the most comprehensive survey of imprinted genes in swine to date.

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“…However its involvement in cancer is not clear. Dong et al (29) defined an expression profile for human hepatocarcinoma. In this assay they showed that SGCE was overexpressed in these tumours in comparison with non-tumour liver.…”

Section: Discussionmentioning

confidence: 99%

MMP-7 and SGCE as distinctive molecular factors in sporadic colorectal cancers from the mutator phenotype pathway

Ortega

Morán²,

Fernández-Marcelo³

et al. 2010

Int J Oncol

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Abstract. Colorectal cancers (CRCs) from the suppressor and the mutator carcinogenic pathways display distinctive pathological and clinical features that remain not completely understood. In this context, the aim of this work was to study the differential expression of metalloproteinases and adhesion molecules related to cancer invasiveness in both groups of tumours. We analyzed 84 tissue specimens, 42 primary sporadic CRCs obtained from patients who underwent radical surgery, and its corresponding control tissues. According to microsatellite instability, 31 cancers showed low or null microsatellite instability (MSI-L/MSS) and 11 tumours displayed high microsatellite instability (MSI-H). Expression assays were established using the Oligo GEArray ® human extracellular matrix and adhesion molecules microarray containing 114 genes. Real-time quantitative PCR (RT-qPCR) confirmed expression data from arrays, using TaqMan probes. Results from oligoarray expression analyses indicated that ITGA3, ITGA9, ITGB4, ITGB7 and MMP15 had significantly higher expression levels in MSI-H tumours versus MSS/ MSI-L cancers, whereas COL12A1, CSPG2, FN1, MMP-7 and SGCE were down-regulated in tumours with high microsatellite instability when compared to the stable group. After RT-qPCR validation, two of these genes, MMP-7 and SGCE, were confirmed to have statistical differences between the two groups of tumours studied. In both cases, MSI-H tumours displayed significant lower expression levels than MSI-L/MSS tumours. In conclusion, these two distinctive molecular markers could be related to a diminished invasion in colorectal tumours from the mutator pathway, this may contribute to the understanding of the better patient prognosis conferred by this type of tumours.

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Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE

Cited by 27 publications

References 36 publications

Identification of Novel Gene Targets and Functions of p21-Activated Kinase 1 during DNA Damage by Gene Expression Profiling

Identification of Novel Gene Targets and Functions of p21-Activated Kinase 1 during DNA Damage by Gene Expression Profiling

Characterization of Conserved and Nonconserved Imprinted Genes in Swine1

MMP-7 and SGCE as distinctive molecular factors in sporadic colorectal cancers from the mutator phenotype pathway

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