Identification of novel long non-coding RNAs in triple-negative breast cancer

Shen, Xiaoxia; Xie, Bojian; Ma, Zhaosheng; Yu, Wenjie; Wang, Wenmin; Xu, Dong; Yan, Xinqiang; Chen, Beibei; Yu, Longyao; Li, Jicheng; Chen, Xiaobing; Ding, Kan; Cao, Feng

doi:10.18632/oncotarget.4419

Cited by 74 publications

(64 citation statements)

References 21 publications

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“…Accumulating evidence indicate that lncRNAs, by interacting with DNA, RNA, protein molecules and/or their combinations, play a critical role in regulation of cellular processes including genetic imprinting, chromatin remodeling, splicing regulation, mRNA decay, transcription, and translational regulation [33-36]. Expression and activity of lncRNAs are deregulated in several types of human cancer, therefore, aberrant expressions of lncRNAs can cause various human diseases, including cancers [34, 37] and contribute to tumor occurrence and development through numerous mechanisms, ranging from epigenetic, transcriptional and posttranscriptional regulation of relevant genes to the control of cell cycle distribution, cell differentiation, and epigenetic modifications [38-41]. Nevertheless, the functions and mechanisms of the vast majority of lncRNAs still remain unknown.…”

Section: Lncrnas In Npcmentioning

confidence: 99%

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

Hann²

2018

Cell Physiol Biochem

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Nasopharyngeal carcinoma (NPC) is one of the most common cancers originating in the nasopharynx and occurring at high frequency in South-eastern Asia and North Africa. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules and key regulators of developmental, physiological, and pathological processes in humans. Emerging studies have shown that lncRNAs play critical roles in tumorgenicity and cancer prognosis. With the development of deep sequencing analyses, an extensive amount of functional lncRNAs have been discovered in nasopharyngeal carcinoma tissues and cell lines. However, the roles and mechanisms of aberrantly expressed lncRNAs in the pathogenesis of NPC are not fully understood. In this review, we briefly illustrate the concept, identification, functional characterization, and summarize recent advancements of biological functions of lncRNAs with heterogeneous mechanistic characterization and their involvement in NPC. Then, we describe individual lncRNAs that have been associated with tumorgenesis, growth, invasion, cancer stem cell differentiation, metastasis, drug resistance and discuss the strategies of their therapeutic manipulation in NPC. We also review the emerging insights into the role of lncRNAs and their potential as biomarkers and therapeutic targets for novel treatment paradigms. Finally, we highlight the up-to-date of clinical information involving lncRNAs and future directions in the linking lncRNAs to potential gene therapies, and how modifications of lncRNAs can be exploited for prevention and treatment of NPC.

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Section: Lncrnas In Npcmentioning

confidence: 99%

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

Hann²

2018

Cell Physiol Biochem

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“…DSCAM-AS1 was identified specifically in ER positive breast tumors and shown to increase aggression and drug resistance (Niknafs et al, 2016). Similarly, AFAP1-AS1 was predominantly found to be dysregulated in HER2 and triple negative breast cancers (TNBC) (Shen et al, 2015;Yang et al, 2016a). H19 was identified to be over-expressed in ER/PR positive breast adenomas and BC200 was implicated to be distinctly elevated in benign tumors and not in invasive subtypes and hence are of prognostic significance (Adriaenssens et al, 1998;Iacoangeli et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Identification of lncRNAs associated with early stage breast cancer and their prognostic implications

Kuha

Patel

et al. 2019

Preprint

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KeywordsLong non-coding RNAs; Breast cancer; ADAMTS9-AS2; FAM83H-AS1; RNA sequencing; ncRNAs Abbreviations DCIS -ductal carcinoma in situ IDC -invasive ductal carcinoma NGS -Next generation sequencing lncRNA -long non-coding RNAs lincRNA -long intergenic non-coding RNA TNBC -Triple negative breast cancers BH -Bonferroni and Benjamini-Hochberg PCA -Principal component analysis PCC -Pearson's correlation coefficient PCG-Protein coding genes AbstractBreast cancer is a common malignancy among women with the highest incidence rate worldwide. Dysregulation of long non-coding RNAs occurring in the preliminary stages of breast carcinogenesis is poorly understood. In this study, RNA sequencing was done to identify long non-coding RNA expression profiles associated with early-stage breast cancer.RNA sequencing was done in 6 invasive ductal carcinoma (IDC) tissues along with paired normal tissue samples, 7 ductal carcinoma in situ (DCIS) tissues and 5 apparently normal breast tissues. We identified 375 differentially expressed lncRNAs (DElncRNAs) in IDC tissues compared to paired normal tissues. Antisense transcripts (~58%) were the largest subtype among DElncRNAs. About 20% of the 375 DElncRNAs were supported by typical split readings leveraging their detection confidence. Validation was done in n=52 IDC and paired normal tissue by qRT-PCR for the identified targets (ADAMTS9-AS2, EPB41L4A-AS1, WDFY3-AS2, RP11-295M3.4, RP11-161M6.2, RP11-490M8.1, CTB-92J24.3 and FAM83H-AS)1. We evaluated the prognostic significance of DElncRNAs based on TCGA datasets and overexpression of FAM83H-AS1 was associated with patient poor survival. We confirmed that the down-regulation of ADAMTS9-AS2 in breast cancer was due to promoter hypermethylation through in-vitro silencing experiments and pyrosequencing.

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“…Shen et al9 have recently reported novel lncRNAs in triple-negative breast cancer. LncRNA expression profile of HER-2-enriched subtype breast cancer has also been analyzed in our previous study 10.…”

Section: Introductionmentioning

confidence: 99%

Identification of lncRNA<em> FAM83H-AS1</em> as a novel prognostic marker in luminal subtype breast cancer

Yang¹,

Lv²,

Lv³

et al. 2016

OTT

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BackgroundLuminal subtype breast cancer accounts for a predominant number of breast cancers. Considering the heterogeneity of the disease, it is urgent to develop novel biomarkers to improve risk stratification and optimize therapy choices. Long non-coding RNA (lncRNA) represents an emerging and understudied class of transcripts that play a significant role in cancer biology. Growing knowledge of cancer-associated lncRNAs contributes to the development of molecular markers for prognosis evaluation and gene therapy.Materials and methodsThree pairs of primary luminal subtype breast cancer tissues and adjacent non-cancerous tissues were collected and sequenced. EBseq algorithm was used to identify differentially expressed lncRNAs. RNA sequencing data from The Cancer Genome Atlas (TCGA) database were used to validate the robustness of our RNA-seq results. Kaplan–Meier and Cox regression analyses were utilized to assess the association between the lncRNAs and overall survival of patients in TCGA cohort.ResultsA total of 796 lncRNAs were significantly dysregulated in luminal subtype breast cancer, including 436 upregulated and 360 downregulated lncRNAs. Among them, FAM83H antisense RNA 1 (FAM83H-AS1) was the most upregulated lncRNA, whereas GSN antisense RNA 1 (GSN-AS1) was the most downregulated lncRNA. Moreover, we proved that the high expression level of FAM83H-AS1 indicated unfavorable prognosis not only in luminal subtype breast cancer but also in all subtype breast cancers. To the best of our knowledge, this is the first report indicating that FAM83H-AS1 was involved in luminal subtype breast cancer and was an independent prognostic indicator.ConclusionOur study provides a rich resource to the research community for further identifying lncRNAs with diagnostic and therapeutic potentials and exploring biological function of lncRNAs in luminal subtype breast cancer.

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Identification of novel long non-coding RNAs in triple-negative breast cancer

Cited by 74 publications

References 21 publications

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

Identification of lncRNAs associated with early stage breast cancer and their prognostic implications

Identification of lncRNA<em> FAM83H-AS1</em> as a novel prognostic marker in luminal subtype breast cancer

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