Identification of unique and common low abundance tumour-specific transcripts by suppression subtractive hybridization and oligonucleotide probe array analysis

Liu, B H; Goh, Christopher; Ooi, London Lucien; Hui, Kam M.

doi:10.1038/onc.2008.50

Cited by 10 publications

(7 citation statements)

References 26 publications

(24 reference statements)

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“…From the results of GSEA (Gene Set Enrichment Analysis) in a published GC cohort NCBI/GEO/GSE62254 ( n = 300) [30], IGF2BP3 upregulation was found to have a positive correlation with expression of a common cancer gene set which was defined by a group of Singaporean researchers ( P < 0.001) [31]. Furthermore, IGF2BP3 was also significantly correlated with cell growth ( P < 0.001) [32] and cell cycle progression ( P = 0.004, Fig.…”

Section: Resultsmentioning

confidence: 99%

IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis

et al. 2017

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BackgroundGastric cancer (GC) is one of the frequent causes of cancer-related death in eastern Asian population. IGF2BP2 lists in the top rank up-regulated genes in GC, but its functional role is unclear.MethodThe expression of IGF2BP3 in GC cell lines and primary samples was examined by qRT-PCR and Western blot. The biological role of IGF2BP3 was revealed by a series of functional in vitro studies. Its regulation by microRNAs (miRNAs) was predicted by TargetScan and confirmed by luciferase assays and rescue experiments.ResultsIGF2BP3 ranked the No.1 of the up-regulated genes by expression microarray analysis in GC cell lines. The expression level of IGF2BP3 was observed in GC tissues comparing with non-tumorous gastric epitheliums. The up-regulated IGF2BP3 expression was associated with poor disease specific survival. IGF2BP3 knockdown significantly inhibited cell proliferation and invasion. Apart from copy number gain, IGF2BP3 has been confirmed to be negatively regulated by tumor-suppressive miRNA, namely miR-34a. The expression of miR-34a showed negative correlation with IGF2BP3 mRNA expression in primary GC samples and more importantly, re-overexpression of IGF2BP3 rescued the inhibitory effect of miR-34a.ConclusionWe compressively revealed the oncogenic role of IGF2BP3 in gastric tumorigenesis and confirmed its activation is partly due to the silence of miR-34a. Our findings identified useful prognostic biomarker and provided clinical translational potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12943-017-0647-2) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis

et al. 2017

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“…Notably, glioblastoma plasticity (Figure S3B) [18], EMT (Figure S3C) [19], tumorigenesis (Figure S3F) [20], tumor anaplastic (Figure S3D) [21], gliomagenesis by platelet derived growth factor B (PDGFB) (Figure S3A) [22], cancer metastasis signature (Figure S3E) [23], common cancer genes (Figure S3G) [24], targets of PTCH1 and SUFU (Figure S3H) and several other gene sets were remarkably enriched in the TACC3 high group, which confirmed the oncogenic role of TACC3 in tumor progression and partially uncovered the potential mechanism (Table S7). …”

Section: Resultsmentioning

confidence: 99%

Overexpression of Transforming Acidic Coiled Coil‑Containing Protein 3 Reflects Malignant Characteristics and Poor Prognosis of Glioma

Sun

Tian

Wang

et al. 2017

IJMS

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Gliomas are malignant primary brain tumors with poor prognosis. Recently, research was indicative of a tight connection between tumor malignancy and genetic alterations. Here, we propose an oncogenic implication of transforming acidic coiled-coil-containing protein 3 (TACC3) in gliomas. By comprehensively analyzing the Chinese glioma genome atlas (CGGA) and publicly available data, we demonstrated that TACC3 were overexpressed along with glioma grade and served as an independent negative prognostic biomarker for glioma patients. Functions’ annotations and gene sets’ enrichment analysis suggested that TACC3 may participate in cell cycle, DNA repair, epithelium-mesenchymal transition and other tumor-related biological processes and molecular pathways. Patients with high TACC3 expression showed CD133+ stem cell properties, glioma plasticity and shorter overall survival time under chemo-/radio-therapy. Additionally, a TACC3 associated the miRNA-mRNA network was constructed based on in silico prediction and expression pattern, which provide a foundation for further detection of TACC3-miRNA-mRNA axis function. Collectively, our observations identify TACC3 as an oncogene of tumor malignancy, as well as a prognostic and motoring biomarker for glioma patients.

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“…The validity of SSH sequences can be confirmed utilizing RT-PCR (Liu et al 2008b), quantitative polymerase chain reaction (qPCR; Yakovlev et al 2008), and the high-throughput method of microarray hybridization. The combination of SSH and microarrays has been successfully used for studying gene expression profiles in several organisms (Cottee et al 2006;Liu et al 2008a). In the present study, we used microarrays, real-time PCR, and RT-PCR as tools to investigate differences in transcription between the adult female and male A. anthropophagus as revealed by SSH.…”

Section: Resultsmentioning

confidence: 99%

Differentially expressed genes between female and male adult Anopheles anthropophagus

et al. 2009

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The aim of the present study was to identify sex-specific genes in adult Anopheles anthropophagus. As the major malaria vector and Brugia malayi vector in the Asian continent, female Anopheles mosquitoes take blood meals and transmit pathogens through this pathway, while males are nectar feeders. This complex behavior is controlled at several levels, but is probably initiated by the genetic background difference between these two groups. In our study, a subtractive cDNA library for female A. anthropophagus was constructed using the suppression subtractive hybridization (SSH) technique and then 3,074 clones from the female SSH library were analyzed using a microarray-based survey. Genes that were expressed differentially according to sex in A. anthropophagus were screened using real-time polymerase chain reaction and reverse transcription polymerase chain reaction. In our results, we report a series of genes which may be involved in female-specific mosquito behavior, including an inorganic phosphate transporter, a serine protease, the salivary protein GP35-2, and the D7 cluster salivary protein. These findings will provide clues to the nature of insect vectors and open up unprecedented opportunities to develop novel strategies for the control of mosquito-borne diseases.

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Identification of unique and common low abundance tumour-specific transcripts by suppression subtractive hybridization and oligonucleotide probe array analysis

Cited by 10 publications

References 26 publications

IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis

IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis

Overexpression of Transforming Acidic Coiled Coil‑Containing Protein 3 Reflects Malignant Characteristics and Poor Prognosis of Glioma

Differentially expressed genes between female and male adult Anopheles anthropophagus

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