Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

Ashouri, Arghavan; Sayin, Volkan I.; Eynden, Jimmy Van den; Singh, Simranjit; Papagiannakopoulos, Thales; Larsson, Erik

doi:10.1038/ncomms13197

Cited by 58 publications

(44 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of note, Ashouri et al recently identified a lncRNA RP11‐115D19.1 (we named it as TRINGS), which is negatively associated with p53 mutation, and exhibited reduced transcription in p53 null cells as compared to p53 wild‐type cells. In addition, expression for this lncRNA (TRINGS) was similarly seen to be reduced in p53‐mutated tumor samples (Ashouri et al , ).…”

Section: Discussionmentioning

confidence: 98%

The p53‐inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation

et al. 2017

View full text Add to dashboard Cite

The tumor suppressor p53 is activated in response to cellular stress to prevent malignant transformation. However, several recent studies have shown that p53 can play protective roles in tumor cell survival under adversity. Whether p53-regulated long noncoding RNAs are involved in this process remains to be fully understood. Here, we show that under glucose starvation condition, p53 directly upregulates a novel lncRNA named TRINGS (Tp53-regulated inhibitor of necrosis under glucose starvation) in human tumor cells. TRINGS binds to STRAP and inhibits STRAP-GSK3b-NF-jB necrotic signaling to protect tumor cells from cell death. Interestingly, TRINGS appears to respond to glucose starvation specifically, as it is not activated by serum, serine, or glutamine deprivation. Collectively, our findings reveal that p53-induced lncRNA TRINGS controls the necrotic pathway and contributes to the survival of cancer cells harboring wild-type p53 under glucose stress.

show abstract

Section: Discussionmentioning

confidence: 98%

The p53‐inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation

et al. 2017

View full text Add to dashboard Cite

show abstract

“…None of the HIF genes were differentially expressed, maybe because the activation of HIF-1 only lasts for a period after cerebral ischemia 43 . A significant downregulated lncRNA in brain-0 and brain-1, RP11-284F21.9 ( Fig.XC), is antisense to BCAN 44 . BCAN (Brevican) encodes a member of proteoglycans that is specifically expressed in CNS, maintaining the extracellular environment of mature brain 45 .…”

Section: Differential Expression Analysis Of Brain Transcriptomesmentioning

confidence: 99%

Analysis of multi-tissue transcriptomes reveals candidate genes and pathways influenced by cerebrovascular diseases

Pan¹,

Chen²

2019

Preprint

View full text Add to dashboard Cite

Cerebrovascular diseases (CVD) are a group of medical conditions that impair circulation of blood to the brain, including stroke, transient ischemic attack (TIA), embolism, aneurysm, and other circulatory disorders affecting the brain. Here, we investigated the effects of having CVD history on the molecular signature of brain regions by comparing gene expression profiles from several brain tissues between cohorts with and without CVD history. We first merged tissue samples from GTEx RNA-Seq dataset into clusters based on the overall gene expression similarity. Then we performed differential expression (DE) analyses for each cluster using a linear mixed model that controls covariates and the individual random effect. Cross-region DE genes were ranked by the combined q-values derived from the mixed model using Fisher's method. Functional enrichment analyses were performed using Gene Set Enrichment Analysis (GSEA) program. We identified hundreds of DE genes, and many of them are related to endothelial or brain functions and associated diseases. We found that STAB1 was highly overexpressed across brain regions in the CVD cohort, and the upregulation of STAB1 in brain tissues may contribute to weaker selfdefense mechanisms against lesions in the brain. Our results suggest a list of candidate genes and pathways that may be dysregulated in the brains of people with CVD history, implying that suffering from CVD could pose potential hazard to the brain.

show abstract

“…RNAseq data and copy number data were downloaded from TCGA and 780 processed as described previously (Ashouri et al 2016). Briefly, RNAseq data 781 were aligned to the human hg19 assembly and quantified using GENCODE 782 (v19) annotated HTSeq-counts and FPKM normalizations.…”

Section: Tcga Data Analysis 779mentioning

confidence: 99%

An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a

Serviss

Richter

Eynden

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

The microRNA-34a is a well-studied tumor suppressor microRNA (miRNA) and a direct downstream target of TP53 with roles in several pathways associated with oncogenesis, such as proliferation, cellular growth, and differentiation. Due to its broad tumor suppressive activity, it is not surprising that miR34a expression is altered in a wide variety of solid tumors and hematological malignancies. However, the mechanisms by which miR34a is regulated in these cancers is largely unknown. In this study, we find that a long non-coding RNA transcribed antisense to the miR34a host gene, is critical for miR34a expression and mediation of its cellular functions in multiple types of human cancer. We name this long non-coding RNA lncTAM34a, and characterize its ability to facilitate miR34a expression under different types of cellular stress in both TP53 deficient and wild type settings.

show abstract

Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

Cited by 58 publications

References 76 publications

The p53‐inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation

The p53‐inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation

Analysis of multi-tissue transcriptomes reveals candidate genes and pathways influenced by cerebrovascular diseases

An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a

Contact Info

Product

Resources

About