Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China

Fang, Weiyi; Li, Xin; Jiang, Qingping; Liu, Zhen; Yang, Huiling; Wang, Shuang; Xie, Shengsong; Liu, Qiuzhen; Liu, Tengfei; Huang, Jing; Xie, Wei‐Bing; Li, Zuguo; Zhao, Yingdong; Wang, Ena; Marincola, Francesco M.; Yao, Kangde

doi:10.1186/1479-5876-6-32

Cited by 158 publications

(147 citation statements)

References 31 publications

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“…Immunohistochemistry was conducted using standard techniques as previously described,25 using a tripartite motif containing 26 (TRIM26) rabbit anti‐human polyclonal antibody (Novus Biologicals). Semiquantitative assessment of staining was carried out independently by two histopathologists.…”

Section: Methodsmentioning

confidence: 99%

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

et al. 2018

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The major histocompatibility complex (MHC) is most closely associated with nasopharyngeal carcinoma (NPC), but the complexity of its genome structure has proven challenging for the discovery of causal MHC loci or genes. We conducted a targeted MHC sequencing in 40 Cantonese NPC patients followed by a two‐stage replication in 1065 NPC cases and 2137 controls of Southern Chinese descendent. Quantitative RT‐PCR analysis (qRT‐PCR) was used to detect gene expression status in 108 NPC and 43 noncancerous nasopharyngeal (NP) samples. Luciferase reporter assay and chromatin immunoprecipitation (ChIP) were used to assess the transcription factor binding site. We discovered that a novel SNP rs117565607_A at TRIM26 displayed the strongest association (OR = 1.909, Pcombined = 2.750 × 10−19). We also observed that TRIM26 was significantly downregulated in NPC tissue samples with genotype AA/AT than TT. Immunohistochemistry (IHC) test also found the TRIM26 protein expression in NPC tissue samples with the genotype AA/AT was lower than TT. According to computational prediction, rs117565607 locus was a binding site for the transcription factor Yin Yang 1 (YY1). We observed that the luciferase activity of YY1 which is binding to the A allele of rs117565607 was suppressed. ChIP data showed that YY1 was binding with T not A allele. Significance analysis of microarray suggested that TRIM26 downregulation was related to low immune response in NPC. We have identified a novel gene TRIM26 and a novel SNP rs117565607_A associated with NPC risk by regulating transcriptional process and established a new functional link between TRIM26 downregulation and low immune response in NPC.

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Section: Methodsmentioning

confidence: 99%

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

et al. 2018

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“…One component included the collection of the microarray profiles from three studies (Supplementary Table S2; refs. 4,5,7). All microarray data were the result of nontreated NPC tissues compared with normal nasopharyngeal tissues.…”

Section: Methodsmentioning

confidence: 99%

“…The etiology of NPC is thought to be associated with a complex interaction of genetic, EBV exposure, environmental, and dietary factors. Although some oncogenes, tumor suppressor genes, and microarray expression data have been previously reported in NPC, a complete understanding of the pathogenesis of NPC in the context of global gene expression remains to be elucidated (1)(2)(3)(4)(5)(6)(7)(8)(9).…”

Section: Introductionmentioning

confidence: 99%

From NPC Therapeutic Target Identification to Potential Treatment Strategy

Lan

Chen

Lin

et al. 2010

Molecular Cancer Therapeutics

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Nasopharyngeal carcinoma (NPC) is relatively rare in Western countries but is a common cancer in southern Asia. Many differentially expressed genes have been linked to NPC; however, how to prioritize therapeutic targets and potential drugs from unsorted gene lists remains largely unknown. We first collected 558 upregulated and 993 downregulated NPC genes from published microarray data and the primary literatures. We then postulated that conversion of gene signatures into the protein-protein interaction network and analyzing the network topologically could provide insight into key regulators involved in tumorigenesis of NPC. Of particular interest was the presence of cliques, called fully connected subgraphs, in the inferred NPC networks. These clique-based hubs, connecting with more than three queries and ranked higher than other nodes in the NPC protein-protein interaction network, were further narrowed down by pathway analysis to retrieve 24 upregulated and 6 downregulated bottleneck genes for predicting NPC carcinogenesis. Moreover, additional oncogenes, tumor suppressor genes, genes involved in protein complexes, and genes obtained after functional profiling were merged with the

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“…(World Health Organization, WHO) NPC incidence rates are less than 1 per 100,000 in most populations, except for those in southern China, where an annual incidence of more than 20 cases per 100,000 is reported. 4 Isolated northern populations, such as Eskimos and Greenlanders, also have high incidences. Moderate incidences occur in North Africa, Israel, Kuwait, the Sudan, and parts of Kenya and Uganda.…”

Section: Ebv-related Cancermentioning

confidence: 99%