Detection of the long noncoding <scp>RNAs</scp> nuclear‐enriched autosomal transcript 1 (<scp>NEAT1</scp>) and metastasis associated lung adenocarcinoma transcript 1 in the peripheral blood of <scp>HIV</scp>‐1‐infected patients

Jin, Changzhong; Peng, Xu; Xie, Tiansheng; Lu, Xiaoyan; Liu, F; Wu, Haibin; Yang, Zhe; Wang, J; Cheng, Liqin; Wu, Na

doi:10.1111/hiv.12276

Cited by 53 publications

(45 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For instance, a well-known and characterized lncRNA, MALAT1 (lnc-SCYL1-1) is found in both datasets and is already linked to viral infection43. In addition, in HIV infected individuals MALAT1 is shown as a potential biomarker44. In this context, it would be worthwhile exploring and comparing transcriptome datasets of other viral infections (i.e.…”

Section: Discussionmentioning

confidence: 99%

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

Trypsteen

Mohammadi

Hecke

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell’s molecular network. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay. Many lncRNAs were suggested to play a role in mechanisms relying on proteasomal and ubiquitination pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis with possible cis regulatory lncRNAs that control nearby mRNA expression and function. Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication.

show abstract

Section: Discussionmentioning

confidence: 99%

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

Trypsteen

Mohammadi

Hecke

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…NEAT1 has been reported to be upregulated in the brains of patients with Huntington's disease (an inherited disorder that results in death of brain cells) and also contains experimentally detected p53 binding sites as TUG1 [23]. NEAT1 was shown to play a role in HIV-1 replication to enhance virus production through increased nucleus-tocytoplasm export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs [49]. Therefore, in HIV+ patients with NCI, the enhanced expression of lncRNA NEAT1 could enhance the HIV-induced neurotoxicity and also lead to the apoptosis of neurons as the role of TUG1.…”

Section: Discussionmentioning

confidence: 99%

WITHDRAWN: Exploring functions of long non-coding RNAs in HIV-associated neurocognitive disorder through weighted gene co-expression network analysis

Wang¹,

Yin²,

Qiu³

et al. 2018

Oncotarget

View full text Add to dashboard Cite

HIV-associated neurocognitive disorder (HAND) remains an unresolved issue of cognitive impairment. Due to treatment with combination antiretroviral therapy for nearly two decades, the severe form of HAND is rare, and most cases of HAND are the milder form. However, the proportion of HIV+ individuals with neurocognitive impairment has remained unchanged. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play important roles in the pathogenesis of several types of neurodegenerative disorders. However, there are few relevant reports about the role of lncRNAs in promoting or delaying pathogenesis of HAND. Our study is the first to use the weighted gene co-expression network analysis approach with microarray data from the Gene Expression Omnibus to investigate the functions of lncRNAs that differ significantly between HIV+ patients without neurocognitive impairment and HIV+ patients with neurocognitive disorders. A total of 28 differentially expressed lncRNAs (DE-lncRNAs) were identified including 13 DE-lncRNAs in frontal white matter, 13 DE-lncRNAs in basal ganglia, and 2 DE-lncRNAs in frontal neocortex. Most of these DE-lncRNAs had not been previously reported to be related to HAND. Our coexpression network and function enrichment analysis indicate that DE-lncRNAs should play fundamental roles in HAND development and neurodegeneration associated with synaptic plasticity and synaptogenesis, neuronal inflammation and apoptosis, neurotransmitter transport and metabolism. Although the biological significance of DE-lncRNAs requires further evaluation, our study proposes a simple and efficient strategy to identify important lncRNAs associated with HAND and predict their potential functional roles, which may guide subsequent experimental studies.

show abstract

“…NEAT1_2 levels have been observed increasing in different cell types following infection with many different RNA viruses, including Japanese encephalitis, rabies [44], HIV [45,46], influenza [38] and hantaan [47], as well as the DNA-encoded herpes simplex virus [48]. In most cases the evidence suggests that NEAT1_2/paraspeckles increase as a cell defence mechanism.…”

Section: Paraspeckles Increase With Viral Infectionmentioning

confidence: 99%

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

Fox

Nakagawa

Hirose

et al. 2018

Trends in Biochemical Sciences

366

338

View full text Add to dashboard Cite

Long noncoding RNA (lncRNA) molecules are some of the newest and least understood players in gene regulation. Hence, we need good model systems with well-defined RNA and protein components. One such system is paraspeckles - protein-rich nuclear organelles built around a specific lncRNA scaffold. New discoveries show how paraspeckles are formed through multiple RNA-protein and protein-protein interactions, some of which involve extensive polymerization, and others with multivalent interactions driving phase separation. Once formed, paraspeckles influence gene regulation through sequestration of component proteins and RNAs, with subsequent depletion in other compartments. Here we focus on the dual aspects of paraspeckle structure and function, revealing an emerging role for these dynamic bodies in a multitude of cellular settings.

show abstract

Detection of the long noncoding RNAs nuclear‐enriched autosomal transcript 1 (NEAT1) and metastasis associated lung adenocarcinoma transcript 1 in the peripheral blood of HIV‐1‐infected patients

Abstract: Our findings suggest that NEAT1 and MALAT1 may interact with HIV-1 in vivo and that the presence of NEAT1 in plasma is a potential biomarker of HIV-1 infection.

Cited by 53 publications

References 15 publications

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

WITHDRAWN: Exploring functions of long non-coding RNAs in HIV-associated neurocognitive disorder through weighted gene co-expression network analysis

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

Contact Info

Product

Resources

About