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High temporal resolution RNA-seq time series of serum-starved T98G human glioblastoma cells responding to serum stimulation

ABSTRACT: The advent of next-generation sequencing revealed extensive transcription outside the boundaries of annotated protein-coding genes, giving rise to tens of thousands of long non-coding RNAs (lncRNAs). The functional relevance of these transcripts remains unclear. Compellingly, lncRNA expression is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory roles. To investigate whether these regulatory roles exist, we examine in detail the timing of lncRNA expression relative to transcripts of known function. If a causal cis-regulatory relationship exists, lncRNA activation must necessarily precede changes in adjacent target gene expression. Here, we report a high temporal resolution RNA-seq time course of synchronized T98G human glioblastoma cells responding to serum stimulation. Detailed profiling of the expression dynamics of lncRNAs and protein-coding genes in these synchronized transitioning human cells provides insight into the feasibility of broad-scale cis-regulatory roles for lncRNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138662 | GEO | 2022/06/23

REPOSITORIES: GEO

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Project description:Recent studies show that long non-coding RNAs (lncRNAs) play crucial roles in human cancers. However, functional lncRNAs and their downstream mechanisms are largely unknown in the molecular pathogenesis of intrahepatic cholangiocarcinoma (ICC) and its progression. In the present study, we performed transcriptomic profiling of five ICC and paired adjacent noncancerous tissues (N) using lncRNA and mRNA microarrays to identify relevant biomarkers in ICC. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the microarray results. We sought correlations between the expression levels of lncRNAs and those of target genes. Clinicopathological characteristics and overall survival were compared using the t-test and the Kaplan–Meier method, respectively. A total of 3,054 and 2,111 lncRNAs were significantly up- and down-regulated(fold change?2, p?0.05) in ICC tissues compared to the adjacent NT samples. Bioinformatic analysis indicated that most such genes were related to carcinogenesis, hepatic system disease, and signal transduction. Positive correlations were evident between four pairs of lncRNAs and target mRNAs (RNA43085 and SULF1, RNA47504 and KDM8, RNA58630 and PCSK6, and RNA40057 and CYP2D6). In addition, some lncRNAs and mRNAs were significantly associated with clinicopathological characteristics. The cumulative overall survival rate was significantly associated with low-level expression of CYP2D6 (p=0.005) and PCSK6 (p=0.038). And patients with high expression levels of CYP2D6 and RNA40057 have significant better prognosis (p=0.014). Our results suggested that lncRNA expression profile in ICC tissues is profoundly different from that in NT samples. The lncRNA signature could be used as a biomarker for the prognosis of patients with ICC. Furthermore, the combination of lncRNA and mRNA can reliably predict the survival. The lncRNA expression profiles of cancer and adjacent normal tissues form 5 ICC patients were studied by microarray and an combination of lncRNA and mRNA could be used as a biomarker for the prognosis of patients with ICC

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High temporal resolution RNA-seq time series of serum-starved T98G human glioblastoma cells responding to serum stimulation

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