Abstract
Simple SummaryLong non-coding RNAs (lncRNA) have been associated with a number of diseases including cancer. A well-studied lncRNA called XIST (X-inactive specific transcript) acts as a major effector of the X-inactivation process. It is expressed on the inactive X chromosome providing a dosage equivalence between males and females. Recently XIST has been implicated in the development of lung cancer. Using a bioinformatics approach, we demonstrate the XIST is over-expressed in female patients compared to males. When XIST gene was silenced in two different cell lines (of male and female origin), a number of genes were differentially expressed; playing a role in signal transduction pathways, energy balance and metabolism, thus providing a better insight of the role of this lncRNA in cancer. Finally, we showed that expression of XIST with another 4 genes provided a strong diagnostic potential to discriminate lung cancer from healthy controls.Long non-coding RNAs (lncRNAs) perform a wide functional repertoire of roles in cell biology, ranging from RNA editing to gene regulation, as well as tumour genesis and tumour progression. The lncRNA X-inactive specific transcript (XIST) is involved in the aetiopathogenesis of non-small cell lung cancer (NSCLC). However, its role at the molecular level is not fully elucidated. The expression of XIST and co-regulated genes TSIX, hnRNPu, Bcl-2, and BRCA1 analyses in lung cancer (LC) and controls were performed in silico. Differentially expressed genes (DEGs) were determined using RNA-seq in H1975 and A549 NSCLC cell lines following siRNA for XIST. XIST exhibited sexual dimorphism, being up-regulated in females compared to males in both control and LC patient cohorts. RNA-seq revealed 944 and 751 DEGs for A549 and H1975 cell lines, respectively. These DEGs are involved in signal transduction, cell communication, energy pathways, and nucleic acid metabolism. XIST expression associated with TSIX, hnRNPu, Bcl-2, and BRCA1 provided a strong collective feature to discriminate between controls and LC, implying a diagnostic potential. There is a much more complex role for XIST in lung cancer. Further studies should concentrate on sex-specific changes and investigate the signalling pathways of the DEGs following silencing of this lncRNA.
Highlights
The large-scale genome sequencing studies of the last decade have documented the pervasiveThe large-scale genome sequencing studies of the last decade have documented the pervasive transcription of almost 90% of the human genome [1], with 98% of the transcriptome consisting of transcription of almost 90% of the human genome [1], with 98% of the transcriptome consisting of long non-coding RNAs [2]
Leveraging the available expression data from The Cancer Genome Atlas project (TCGA) and GTEX, as tumour and respectively normal control lung samples, we have investigated differential expression patterns of X-inactive specific transcript (XIST), TSIX, heterogeneous nuclear ribonucleoprotein U (hnRNPu), B-cell lymphoma 2 (Bcl-2), and BRAC1 in lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC) (Supplementary Figure S1)
Similar to previously published results where XIST is upregulated in various cancers [6,30], we found a similar trend, in LUAD compared to normal lung cohort (LUNG), whereas in LUSC a downregulation was observed (Figure 2a)
Summary
The large-scale genome sequencing studies of the last decade have documented the pervasive transcription of almost 90% of the human genome [1], with 98% of the transcriptome consisting of transcription of almost 90% of the human genome [1], with 98% of the transcriptome consisting of long non-coding RNAs (lncRNAs) [2]. Despite these efforts, our current understanding of long non-coding RNAs (lncRNAs) [2]. Previous analyses analyses have pointed to a wide range of functions for lncRNAs in developmental and cellular have pointed to a wide range of functions for lncRNAs in developmental and cellular processes, processes, including gene expression, chromatin remodeling and modification, splicing, editing, including gene expression, chromatin remodeling and modification, splicing, editing, translation and translation and degradation of the RNA, and gene silencing with endogenous small interfering RNA degradation of the RNA, and gene silencing with endogenous small interfering RNA (siRNA) [4,5,6]
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