Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations

Background

Integrative analysis of endometrioid endometrial carcinoma (EEC) using multiple platforms has distinguished four molecular subgroups. However, the landscape of expressed long non-coding RNAs (lncRNA) and their role in charting EEC subgroups and determining clinical aggressiveness remain largely unknown.

Materials and Methods

We performed integrative analysis of lncRNAs in EEC using The Cancer Genome Atlas (TCGA) molecular RNAseq profiles of 191 primary tumors for which genomic data were also available. We established lncRNA subgroup classification, correlated it with chromatin modifying gene expression, and described correlations between our lncRNA classification and clinico-genomic tumor features.

Results

Using stringent criteria, we identified 1,931 expressed lncRNAs and predicted potential drivers through integrative analysis. Unsupervised clustering of lncRNA expression revealed three robust categories: basal-like, luminal-like and CTNNB1-enriched subgroups. Basal-like subgroup was enriched for aggressive tumors with higher pathological grade (p < 0.0001), TNM stage (p = 0.01), and somatic mutations in trithorax-group genes (MLL, MLL2 and MLL3); and it overexpressed polycomb genes EZH2 and CBX2. In contrast to the luminal-like subgroup, progesterone (PGR) and estrogen receptor (ESR1) genes were highly down-regulated in the EEC basal-like subgroup. Consistent with its enrichment for CTNNB1 mutations (69%), lncRNA profile of the CTNNB1-enriched EEC subgroup was highly similar to that of the CTNNB1-enriched liver cancer subgroup.

Conclusions

Our results reveal the utility of systematic characterization of clinically annotated EEC in three clinically relevant subgroups. They also highlight the convergence of aberrations in polycomb- and trithorax-group genes in aggressive basal EEC subtypes, providing a rationale for further investigation of epigenetic therapy in this setting.     

HOTAIR: an oncogenic long non-coding RNA in different cancers

Long non-coding RNAs (lncRNAs) refer to a group of RNAs that are usually more than 200 nucleotides and are not involved in protein generation. Instead, lncRNAs are involved in different regulatory processes, such as regulation of gene expression. Different lncRNAs exist throughout the genome. LncRNAs are also known for their roles in different human diseases such as cancer. HOTAIR is an lncRNA that plays a role as an oncogenic molecule in different cancer cells, such as breast, gastric, colorectal, and cervical cancer cells. Therefore, HOTAIR expression level is a potential biomarker for diagnostic and therapeutic purposes in several cancers. This RNA takes part in epigenetic regulation of genes and plays an important role in different cellular pathways by interacting with Polycomb Repressive Complex 2 (PRC2). In this review, we describe the molecular function and regulation of HOTAIR and its role in different types of cancers.KEYWORDS : HOTAIR, long non-coding RNA (lncRNA), epigenetic, cancer     

Upregulated long non-coding RNA AFAP1-AS1 expression is associated with progression and poor prognosis of nasopharyngeal carcinoma

Altered expression of long noncoding RNAs (lncRNAs) associated with human carcinogenesis. We performed a cDNA microarray analysis of lncRNA expression in 12 cases of nasopharyngeal carcinoma (NPC) and 4 non-tumor nasopharyngeal epitheliums. One lncRNA, actin filament associated protein 1 antisense RNA1 (AFAP1-AS1), was identified and selected for further study. AFAP1-AS1 expression was upregulated in NPC and associated with NPC metastasis and poor prognosis. In vitro experiments demonstrated that AFAP1-AS1 knockdown significantly inhibited the NPC cell migration and invasive capability. AFAP1-AS1 knockdown also increased AFAP1 protein expression. Proteomic and bioinformatics analyses suggested that AFAP1-AS1 affected the expression of several small GTPase family members and molecules in the actin cytokeratin signaling pathway. AFAP1-AS1 promoted cancer cell metastasis via regulation of actin filament integrity. AFAP1-AS1 might be a potential novel marker that can predict cancer patient prognosis and as a potential therapeutic target for NPC.     

四种长链非编码RNA在乳腺癌中的表达及与患者预后的关系CSCD

目的探讨EGOT、MEG3、KCNQ1OT1和NEAT1四种LncRNA在不同亚型乳腺癌患者中的表达及与患者临床病理特征及预后的关系。方法利用UALCAN网站挖掘TCGA数据库等大数据,分析四种LncRNA在1097个乳腺癌组织样本和114个正常组织样本中的表达,用Kaplan-Meier Plotter法绘制生存曲线,分析四种LncRNA与乳腺癌患者预后的关系。通过LinkedOmics网站和ClueGO工具分析与它们表达相关的蛋白质的主要功能。结果EGOT、MEG3在乳腺癌组织中的表达显著低于正常组织(P<0.05);HER2阳性乳腺癌中KCNQ1OT1显著低表达(P<0.05);NEAT1在Ⅳ期、HER2阳性和三阴性乳腺癌中的表达显著低于正常组织(P<0.05)。四种LncRNA的表达水平与乳腺癌患者的无复发生存时间(RFS)均有显著相关性(P<0.05),且LncRNA低表达时乳腺癌患者的RFS和预后较差。通过功能富集分析发现与四种LncRNA表达相关的蛋白质均与重要生物过程或通路相关。结论四种LncRNA在乳腺癌或部分亚型中表达下调,它们可能是乳腺癌中潜在的抑癌因子,且可成为判断乳腺癌患者预后的生物学指标。     

Progress and assessment of lncRNA DGCR5 in malignant phenotype and immune infiltration of human cancers

As a special type of noncoding RNA, long noncoding RNAs (lncRNAs) have vital roles during the development of human cancers and may be novel predictors or therapeutic targets for improving the management of patients with cancer. DiGeorge syndrome critical region gene 5 (DGCR5) is a prominent tumor-associated lncRNA, exerting tumor suppressor or oncogenic roles in various cancers. Previous studies have reported that DGCR5 has low expression in most types of cancers but high expression in triple-negative breast cancer, gallbladder cancer, and lung cancer. And DGCR5 expression is related to many hallmarks of cancer types, including cell proliferation, invasion, migration, apoptosis, stemness, and therapeutic responsiveness. Additionally, the pivotal molecules involved in DGCR5 regulation of signaling pathways are attributed to cancer hallmarks related to the pathogenesis of different types of malignant tumors. Herein, we discuss the DGCR5 expression pattern in various types of tumor tissues and relationships between DGCR5 expression and immune cell infiltration and immune purity. We also review our current understanding of DGCR5 in carcinogenesis and its potential application as a prognostic biomarker or therapeutic target in human cancers.     

MYC-binding lncRNA EPIC1 promotes AKT-mTORC1 signaling and rapamycin resistance in breast and ovarian cancer

AKT-mTORC1 (mammalian target of rapamycin complex 1) signaling pathway plays a critical role in tumorigenesis and can be targeted by rapamycin. However, the underlying mechanism of how long noncoding RNA (lncRNAs) regulate the AKT-mTORC1 pathway remains unclear. EPIC1 (epigenetically-induced lncRNA 1) is a Myc-binding lncRNA, which has been previously demonstrated to be overexpressed in multiple cancer types. In a pathway analysis including 4962 cancer patients, we observed that lncRNA EPIC1 expression was positively correlated with the AKT-mTORC1 signaling pathway in more than 10 cancer types, including breast and ovarian cancers. RNA-seq analysis of breast and ovarian cancer cells demonstrated that EPIC1-knockdown led to the downregulation of genes in the AKT-mTORC1 signaling pathway. In MCF-7, OVCAR4, and A2780cis cell lines, EPIC1 knockdown and overexpression, respectively, inhibited and activated phosphorylated AKT and the downstream phosphorylation levels of 4EBP1 and S6K. Further knockdown of Myc abolished the EPIC1′s regulation of AKT-mTORC1 signaling; suggested that the regulation of phosphorylation level of AKT, 4EBP1, and S6K by EPIC1 depended on the expression of Myc. Moreover, EPIC1 overexpressed MCF-7, A2780cis, and OVCAR4 cells treated with rapamycin showed a significant decreasing in rapamycin mediated inhibition of p-S6K and p-S6 comparing with the control group. In addition, Colony Formation assay and MTT assay indicated that EPIC1 overexpression led to rapamycin resistance in breast and ovarian cancer cell lines. Our results demonstrated the lncRNA EPIC1 expression activated the AKT-mTORC1 signaling pathway through Myc and led to rapamycin resistance in breast and ovarian cancer.     

乳腺癌竞争内源性RNA网络构建与分析

目的:通过对癌症基因组图谱(The Cancer Genome Atlas，TCGA)数据库中的乳腺癌数据进行综合分析，寻找在乳腺癌中差异表达的长链非编码RNA(long non-coding RNA，lncRNA）、微小RNA（microRNA，miRNA）和信使RNA（messenger RNA，mRNA），构建乳腺癌竞争内源性RNA（competing endogenous RNA，ceRNA）网络，识别和预测ceRNA网络在乳腺癌中的作用。方法:下载TCGA数据库中乳腺癌组织样本基因表达谱数据，寻找差异表达的lncRNA、miRNA和mRNA，通过miRcode、miRTarBase、TargetScan和miRDB四个数据库对差异表达的RNA之间的关系进行分析，构建以上调和下调的miRNA为中心的ceRNA网络。采用Kaplan-Meier法分析乳腺癌ceRNA网络中的lncRNA、miRNA和mRNA表达量与患者生存预后的关系，采用基因富集分析法对乳腺癌ceRNA网络中mRNA基因功能和调控通路进行分析。结果:在乳腺癌中异常表达的350个lncRNA、185个miRNA和2 928个mRNA中，分别有23个lncRNA、27个miRNA、70个mRNA参与构建乳腺癌的ceRNA网络。Kaplan-Meier生存分析显示，lncRNA MAGI2-AS3（P=0.01）、GRIK1-AS1（P=0.03）以及miRNA hsa-miR-301b（P=0.01）、hsa-miR-503（P=0.04）和mRNA CCNE1（P=0.01）、KPNA2（P=0.02）、FLI1（P=0.02）、TGFBR2（P=0.02）这8个基因与乳腺癌患者的生存预后显著相关。70个mRNA主要被富集到20条通路上，其中有15条通路与肿瘤有关，最显著的通路为“Pathways in cancer”。结论:ceRNA网络在乳腺癌中发挥着重要的作用，多种差异表达基因与乳腺癌预后相关，可能成为潜在的肿瘤诊断标志物和治疗靶点。     

Aberrant allele-switch imprinting of a novel IGF1R intragenic antisense non-coding RNA in breast cancers

The insulin-like growth factor type I receptor (IGF1R) is frequently dysregulated in breast cancers, yet the molecular mechanisms are unknown. A novel intragenic long non-coding RNA (lncRNA) IRAIN within the IGF1R locus has been recently identified in haematopoietic malignancies using RNA-guided chromatin conformation capture (R3C). In breast cancer tissues, we found that IRAIN lncRNA was transcribed from an intronic promoter in an antisense direction as compared to the IGF1R coding mRNA. Unlike the IGF1R coding RNA, this non-coding RNA was imprinted, with monoallelic expression from the paternal allele. In breast cancer tissues that were informative for single nucleotide polymorphism (SNP) rs8034564, there was an imbalanced expression of the two parental alleles, where the ‘G’ genotype was favorably imprinted over the ‘A’ genotype. In breast cancer patients, IRAIN was aberrantly imprinted in both tumours and peripheral blood leucocytes, exhibiting a pattern of allele-switch: the allele expressed in normal tissues was inactivated and the normally imprinted allele was expressed. Epigenetic analysis revealed that there was extensive DNA demethylation of CpG islands in the gene promoter. These data identify IRAIN lncRNA as a novel imprinted gene that is aberrantly regulated in breast cancer.     

Induction of epithelial-mesenchymal transition (EMT) by hypoxia-induced lncRNA RP11-367G18.1 through regulating the histone 4 lysine 16 acetylation (H4K16Ac) mark

Hypoxia activates various long noncoding RNAs (lncRNAs) to induce the epithelial-mesenchymal transition (EMT) and tumor metastasis. The hypoxia/HIF-1α-regulated lncRNAs that also regulate a specific histone mark and promote EMT and metastasis have not been identified. We performed RNA-sequencing dataset analysis to search for such lncRNAs and lncRNA RP11-367G18.1 was the hypoxia-induced lncRNA with the highest hazard ratio. High expression of lncRNA RP11-367G18.1 is correlated with a worse survival of head and neck cancer patients. We further showed that lncRNA RP11-367G18.1 is induced by hypoxia and directly regulated by HIF-1α in cell lines. Overexpression of lncRNA RP11-367G18.1 induces the EMT and increases the in vitro migration and invasion and in vivo metastatic activity. Knockdown experiments showed that lncRNA RP11-367G18.1 plays an essential role in hypoxia-induced EMT. LncRNA RP11-367G18.1 specifically regulates the histone 4 lysine 16 acetylation (H4K16Ac) mark that is located on the promoters of two “core” EMT regulators, Twist1 and SLUG, and VEGF genes. These results indicate that lncRNA RP11-367G18.1 regulates the deposition of H4K16Ac on the promoters of target genes to activate their expression. This report identifies lncRNA RP11-367G18.1 as a key player in regulating the histone mark H4K16Ac through which activates downstream target genes to mediate hypoxia-induced EMT.     

MicroRNA-101 inhibits cell progression and increases paclitaxel sensitivity by suppressing MCL-1 expression in human triple-negative breast cancer

Triple-negative breast cancer is the most aggressive breast cancer subtype. The aim of our study was to investigate the functional role of both miR-101 and MCL-1 in the sensitivity of human triple-negative breast cancer (TNBC) to paclitaxel. We found that the expression of miR-101 was strongly decreased in triple-negative breast cancer tissues and cell lines. The expression of miR-101 was not associated with clinical stage or lymph node infiltration in TNBC. Ectopic overexpression of miR-101 inhibit growth and induced apoptosis in vitro and suppressed tumorigenicity in vivo. MCL-1 was significantly overexpressed in most of the TNBC tissues and cell lines. Luciferase assay results confirmed MCL-1 as a direct target gene of miR-101. MiR-101 inhibited MCL-1 expression in TNBC cells and transplanted tumors. There was a negative correlation between the level of expression of miR-101 and MCL-1 in TNBC tissues. Suppression of MCL-1 enhanced the sensitivity of MDA-MB-435 cells to paclitaxel. Furthermore, miR-101 increased paclitaxel sensitivity by inhibiting MCL-1 expression. Our findings provide significant insight into the molecular mechanisms of TNBC carcinogenesis and may have clinical relevance for the development of novel, targeted therapies for TNBC.