Epstein–Barr virus-encoded small RNA 1 (EBER-1) could predict good prognosis in nasopharyngeal carcinoma

Zeng, Zhaoyang; Fan, Songquing; Zhang, X.; Li, S.; Zhou, Ming; Wang, Xiong; Tan, Ming; Zhang, W.; Li, G.

doi:10.1007/s12094-015-1354-3

Cited by 46 publications

(31 citation statements)

References 36 publications

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“…LncRNAs compose a large set of RNA molecules that exceed 200 nt in length, completely lack or possess limited protein-coding capacity, and represent a substantial portion of the transcriptome [65][66][67][68][69][70][71][72]. LncRNAs widely regulate gene expression at the epigenetic, transcriptional, and post-transcriptional levels.…”

Section: Discussionmentioning

confidence: 99%

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Xiong

Zhou

et al. 2015

Mol Cell Biochem

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BRD7 is a single bromodomain-containing protein that functions as a subunit of the SWI/SNF chromatin-remodeling complex to regulate transcription. It also interacts with the well-known tumor suppressor protein p53 to trans-activate genes involved in cell cycle arrest. In this paper, we report an integrative analysis of genome-wide chromatin occupancy of BRD7 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and digital gene expression (DGE) profiling by RNA-sequencing upon the overexpression of BRD7 in human cells. We localized 156 BRD7-binding peaks representing 184 genes by ChIP-sequencing, and most of these peaks were co-localized with histone modification sites. Four novel motifs were significantly represented in these BRD7-enriched regions. Ingenuity pathway analysis revealed that 22 of these BRD7 target genes were involved in a network regulating cell death and survival. DGE profiling identified 560 up-regulated genes and 1088 down-regulated genes regulated by BRD7. Using Gene Ontology and pathway analysis, we found significant enrichment of the cell cycle and apoptosis pathway genes. For the integrative analysis of the ChIP-seq and DEG data, we constructed a regulating network of BRD7 downstream genes, and this network suggests multiple feedback regulations of the pathways. Furthermore, we validated BIRC2, BIRC3, TXN2, and NOTCH1 genes as direct, functional BRD7 targets, which were involved in the cell cycle and apoptosis pathways. These results provide a genome-wide view of chromatin occupancy and the gene regulation network of the BRD7 signaling pathway.

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Section: Discussionmentioning

confidence: 99%

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Xiong

Zhou

et al. 2015

Mol Cell Biochem

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“…8,9 Workup for NPC may include EBV testing of both the tumor itself and the blood, particularly in the presence of nonkeratinizing and undifferentiated histology. [10][11][12] Testing methods for detection of EBV in the tumor include in situ hybridization for EBV-encoded RNA 13 and immunohistochemical staining for LMP1. 14 The former tends to be a more sensitive testing method for carcinomas, relative to LMP1 immunohistochemical staining.…”

Section: Epstein-barr Virusmentioning

confidence: 99%

NCCN Guidelines Insights: Head and Neck Cancers, Version 1.2018

Colevas¹,

Yom²,

Pfister³

et al. 2018

J Natl Compr Canc Netw

472

411

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The NCCN Guidelines for Head and Neck (H&N) Cancers provide treatment recommendations for cancers of the lip, oral cavity, pharynx, larynx, ethmoid and maxillary sinuses, and salivary glands. Recommendations are also provided for occult primary of the H&N, and separate algorithms have been developed by the panel for very advanced H&N cancers. These NCCN Guidelines Insights summarize the panel's discussion and most recent recommendations regarding evaluation and treatment of nasopharyngeal carcinoma.

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“…They regulate gene expression through transcriptional, post-transcriptional and epigenetic effects [2–8]. Tens of thousands of lncRNAs have been identified in the human genome [9], many of which are abnormally expressed in a variety of human tumors, and are involved in various stages of carcinogenesis, including tumor initiation, progression and metastasis [10–17]. However, the function of the vast majority of these lncRNAs is still unclear.…”

Section: Introductionmentioning

confidence: 99%

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

et al. 2017

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Nasopharyngeal carcinoma (NPC) carries a high potential for metastasis and immune escape, with a great risk of relapse after primary treatment. Through analysis of whole genome expression profiling data in NPC samples, we found that the expression of a long non-coding RNA (lncRNA), actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1), is significantly correlated with the immune escape marker programmed death 1 (PD-1). We therefore assessed the expression of AFAP1-AS1 and PD-1 in a cohort of 96 paraffin-embedded NPC samples and confirmed that AFAP1-AS1 and PD-1 are co-expressed in infiltrating lymphocytes in NPC tissue. Moreover, patients with high expression of AFAP1-AS1 or PD-1 in infiltrating lymphocytes were more prone to distant metastasis, and NPC patients with positive expression of both AFAP1-AS1 and PD-1 had the poorest prognosis. This study suggests that AFAP1-AS1 and PD-1 may be potential therapeutic targets in NPC and that patients with co-expression of AFAP1-AS1 and PD-1 may be ideal candidates for future clinical trials of anti-PD-1 immune therapy.

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Epstein–Barr virus-encoded small RNA 1 (EBER-1) could predict good prognosis in nasopharyngeal carcinoma

Abstract: These results indicated that EBER-1 expression is a potential prognosis factor of NPC and highly negative correlated with the progress of NPC.

Cited by 46 publications

References 36 publications

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

NCCN Guidelines Insights: Head and Neck Cancers, Version 1.2018

Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma

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