scholarly journals Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer

2017 ◽  
Author(s):  
Pieter-Jan Volders ◽  
Jo Vandesompele ◽  
Steve Lefever ◽  
Shalina Baute ◽  
Justine Nuytens ◽  
...  
Keyword(s):  
Copy Number ◽  
Human Cancer ◽  
Microarray Platform ◽  
Copy Number Alterations ◽  
Protein Coding ◽  
Lncrna Gene ◽  
Cancer Pathogenesis ◽  
Non Coding Rna ◽  
Long Non Coding Rna

AbstractThe landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancer remains largely unexplored. While the majority of lncRNAs remains to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that is currently reported, it is conceivable that several lncRNAs might function as oncogenes or tumor suppressor genes.We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 20 418 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs involved in cancer pathogenesis.

scholarly journals Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines

2018 ◽  
Vol 4 (3) ◽  
pp. 21 ◽  
Author(s):  
Pieter-Jan Volders ◽  
Steve Lefever ◽  
Shalina Baute ◽  
Justine Nuytens ◽  
Katrien Vanderheyden ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Copy Number ◽  
Microarray Platform ◽  
Cancer Cell Lines ◽  
Copy Number Alterations ◽  
Protein Coding ◽  
Lncrna Gene ◽  
Cancer Pathogenesis ◽  
Non Coding Rna

The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancers remains largely unexplored. While the majority of lncRNAs remain to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that have been currently reported, it is conceivable that many more lncRNAs might function as oncogenes or tumor suppressor genes. We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 10,519 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs that are involved in cancer pathogenesis.

scholarly journals Long non-coding RNA LINC00665 promotes gemcitabine resistance of Cholangiocarcinoma cells via regulating EMT and stemness properties through miR-424-5p/BCL9L axis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Min Lu ◽  
Xinglei Qin ◽  
Yajun Zhou ◽  
Gang Li ◽  
Zhaoyang Liu ◽  
...  
Keyword(s):  
Acquired Resistance ◽  
Transcriptional Regulators ◽  
First Line ◽  
Protein Coding ◽  
Gemcitabine Resistance ◽  
Non Coding Rna ◽  
Sphere Formation ◽  
Long Non Coding Rna ◽  
Line Chemotherapy

AbstractGemcitabine is the first-line chemotherapy drug for cholangiocarcinoma (CCA), but acquired resistance has been frequently observed in CCA patients. To search for potential long noncoding RNAs (lncRNAs) involved in gemcitabine resistance, two gemcitabine resistant CCA cell lines were established and dysregulated lncRNAs were identified by lncRNA microarray. Long intergenic non-protein coding RNA 665 (LINC00665) were found to rank the top 10 upregulated lncRNAs in our study, and high LINC00665 expression was closely associated with poor prognosis and chemoresistance of CCA patients. Silencing LINC00665 in gemcitabine resistant CCA cells impaired gemcitabine tolerance, while enforced LINC00665 expression increased gemcitabine resistance of sensitive CCA cells. The gemcitabine resistant CCA cells showed increased EMT and stemness properties, and silencing LINC00665 suppressed sphere formation, migration, invasion and expression of EMT and stemness markers. In addition, Wnt/β-Catenin signaling was activated in gemcitabine resistant CCA cells, but LINC00665 knockdown suppressed Wnt/β-Catenin activation. B-cell CLL/lymphoma 9-like (BCL9L), the nucleus transcriptional regulators of Wnt/β-Catenin signaling, plays a key role in the nucleus translocation of β-Catenin and promotes β-Catenin-dependent transcription. In our study, we found that LINC00665 regulated BCL9L expression by acting as a molecular sponge for miR-424-5p. Moreover, silencing BCL9L or miR-424-5p overexpression suppressed gemcitabine resistance, EMT, stemness and Wnt/β-Catenin activation in resistant CCA cells. In conclusion, our results disclosed the important role of LINC00665 in gemcitabine resistance of CCA cells, and provided a new biomarker or therapeutic target for CCA treament.

scholarly journals HOTAIR: An Oncogenic Long Non-Coding RNA in Human Cancer

2018 ◽  
Vol 47 (3) ◽  
pp. 893-913 ◽  
Author(s):  
Qing Tang ◽  
Swei Sunny Hann
Keyword(s):  
Drug Resistance ◽  
Human Cancer ◽  
Critical Role ◽  
Stem Cell Differentiation ◽  
Human Diseases ◽  
Biological Functions ◽  
Protein Coding ◽  
Non Coding Rna ◽  
And Function ◽  
Long Non Coding Rna

Long non-coding RNAs (LncRNAs) represent a novel class of noncoding RNAs that are longer than 200 nucleotides without protein-coding potential and function as novel master regulators in various human diseases, including cancer. Accumulating evidence shows that lncRNAs are dysregulated and implicated in various aspects of cellular homeostasis, such as proliferation, apoptosis, mobility, invasion, metastasis, chromatin remodeling, gene transcription, and post-transcriptional processing. However, the mechanisms by which lncRNAs regulate various biological functions in human diseases have yet to be determined. HOX antisense intergenic RNA (HOTAIR) is a recently discovered lncRNA and plays a critical role in various areas of cancer, such as proliferation, survival, migration, drug resistance, and genomic stability. In this review, we briefly introduce the concept, identification, and biological functions of HOTAIR. We then describe the involvement of HOTAIR that has been associated with tumorigenesis, growth, invasion, cancer stem cell differentiation, metastasis, and drug resistance in cancer. We also discuss emerging insights into the role of HOTAIR as potential biomarkers and therapeutic targets for novel treatment paradigms in cancer.

scholarly journals The emerging role of long non-coding RNA in gallbladder cancer pathogenesis

Biochimie ◽  
2017 ◽  
Vol 132 ◽  
pp. 152-160 ◽  
Author(s):  
Akanksha Khandelwal ◽  
Akshay Malhotra ◽  
Manju Jain ◽  
Karen M. Vasquez ◽  
Aklank Jain
Keyword(s):  
Gallbladder Cancer ◽  
Cancer Pathogenesis ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Long non-coding RNAs and splicing

2021 ◽  
Author(s):  
David Staněk
Keyword(s):  
Dominant Role ◽  
Splice Sites ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Splicing Efficiency ◽  
Non Coding Rnas ◽  
Intron Removal ◽  
Long Non Coding Rna

Abstract In this review I focus on the role of splicing in long non-coding RNA (lncRNA) life. First, I summarize differences between the splicing efficiency of protein-coding genes and lncRNAs and discuss why non-coding RNAs are spliced less efficiently. In the second half of the review, I speculate why splice sites are the most conserved sequences in lncRNAs and what additional roles could splicing play in lncRNA metabolism. I discuss the hypothesis that the splicing machinery can, besides its dominant role in intron removal and exon joining, protect cells from undesired transcripts.

MP99-18 ROLE OF LONG NON-CODING RNA PVT1 IN REGULATING MYC IN HUMAN CANCER

2017 ◽  
Vol 197 (4S) ◽  
Author(s):  
Kojiro Tashiro ◽  
Yuen-Yi Tseng ◽  
Badrinath Konety ◽  
Anindya Bagchi
Keyword(s):  
Human Cancer ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals The State of Long Non-Coding RNA Biology

2018 ◽  
Vol 4 (3) ◽  
pp. 17 ◽  
Author(s):  
John S. Mattick
Keyword(s):  
Transgenerational Inheritance ◽  
Protein Coding ◽  
Cellular Processes ◽  
Non Coding Rna ◽  
Large Numbers ◽  
Rna Biology ◽  
Subcellular Domains ◽  
Multicellular Organisms ◽  
Long Non Coding Rna

Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure–function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.

scholarly journals A Review on the Role of AFAP1-AS1 in the Pathoetiology of Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Soudeh Ghafouri-Fard ◽  
Tayybeh Khoshbakht ◽  
Bashdar Mahmud Hussen ◽  
Mohammad Taheri ◽  
Majid Mokhtari
Keyword(s):  
Cancer Progression ◽  
Animal Studies ◽  
Human Subjects ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Reduce Tumor Volume ◽  
Xenograft Models ◽  
The Impact ◽  
Long Non Coding Rna

AFAP1-AS1 is a long non-coding RNA which partakes in the pathoetiology of several cancers. The sense protein coding gene from this locus partakes in the regulation of cytophagy, cell motility, invasive characteristics of cells and metastatic ability. In addition to acting in concert with AFAP1, AFAP1-AS1 can sequester a number of cancer-related miRNAs, thus affecting activity of signaling pathways involved in cancer progression. Most of animal studies have confirmed that AFAP1-AS1 silencing can reduce tumor volume and invasive behavior of tumor cells in the xenograft models. Moreover, statistical analyses in the human subjects have shown strong correlation between expression levels of this lncRNA and clinical outcomes. In the present work, we review the impact of AFAP1-AS1 in the carcinogenesis.

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