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ABSTRACT- Long non-coding RNAs (lncRNAs) are a group of longer than 200 nucleotides which are the largest and
more diverse transcripts in the cells. After study from Functional Annotation of Mammalian cDNA, lncRNAs
demonstrated some special characteristics such as lower quantity, higher tissue-specificity, higher stage specificity and
higher cell subtype specificity. The current evidence from tumor diseases suggests that lncRNAs are an important
regulatory RNA present at tumor cells, and therefore their alterations are associated with tumorigenesis and tumor
diseases. Here we presented a clinical landscape of lncRNA including detection of lncRNA and their clinical application
such as diagnosis biomarkers and therapeutic targets. We also discussed the challenges and resolving strategies for these
clinical applications.
Key-words- Long non-coding RNA (lncRNA), Transcripts, sampling, Tumor and tumorigenesis
INTRODUCTION
Long non-coding RNAs (lncRNAs) are some longer than expression profiles so that now human lncRNAs are finally
200 nucleotides in which most of them have not any coding discovered as a bias toward two-exon transcripts[4].
protein function[1]. After several years study from projects Because of lack strong conservation, lncRNA may play an
called as Functional Annotation of Mammalian cDNA adaptive selection in evolutionary pressures or environment
(FANTOMs), 35,000 non-coding transcripts identified from pressures. Total RNA sequencing from cDNA libraries
their projects demonstrated that lncRNAs are 10-fold lower show that very few numbers of lncRNA have biologically
than mRNAs with a little open reading frame (ORF) but translated proteins. As Fig 1, during their RNA
lncRNA structures are similar to mRNAs including 5 transcriptions, lncRNAs target transcriptional activators or
capping, splicing, and polyadenylation[2]. Interestingly, repressors utilized complex such as by Evf-2 functions with
lncRNAs have about 78% tissue-specificity, higher stage a co-activator for the homeobox transcription factor
specificity and higher cell subtype specificity[3] while (D1x2), by CREB binding protein, by HDAC system, by
mRNAs are only about 19% tissue-specificity, lower stage Apolipoprotein A1 (APOA1), by Alu RNA transcripts,
specificity and lower cell subtype specificity. functional repeat sequence domains by Kcnq1ot1, by Xlsirt
LncRNAs sequences are located intergenic genome, and and Xist and heat shock RNA-1 (HSR-1) in which an
therefore they can be transcribed as complex, overlapping RNAP III regulating its RNAP II supports lncRNA
transcripts from protein-coding genes with sense and functional regulation. After transcriptional regulation,
antisense directions. A comprehensive set of human lncRNA also involve in mRNA splicing, transport,
lncRNAs are analyzed and annotated by their genomic translation, and degradation. Besides those, lncRNA also
organization, modifications, cellular locations and tissue play function in siRNAs, epigenetics, imprinting, active
X-chromosome, telomere function. Some lncRNAs maybe
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have their coding proteins but its still under investigation[5].
Quick Response Code Website: In clinical fields, increasing evidence demonstrated that
www.ijlssr.com lncRNA alterations are associated with tumor diseases.
Here I concluded an outline from clinical sampling,
lncRNA detection and clinical application from lncRNAs
aberrance in tumor diseases as Fig 2. In the end of manual,
DOI: 10.21276/ijlssr.2017.3.3.11 I will present some challenges, and therefore I will suggest
some strategies for these future applications.
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Fig. 2: Clinical lncRNA analysis. Process from sampling performance, lncRNA detection and application.
Yellow color means lncRNA prediction and diagnosis which will be discussed in details in the manual
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Advantages An easily accessible, minimally invasive way Higher Specificity and sensitivity
There are two ways to detect lncRNA expressions: experiments in tumor diseases [7]. RNA FISH is a cyto
(a) specific lncRNA detection by either real time PCR or genetic technique that uses fluorescent probe to bind to
lncRNA FISH and (b) genomic detection by either lncRNA with a high degree of sequence complementarity
microarray or next-generation RNA sequencing. Because as Fig 3B. Fluorescence microscope can find out where the
lncRNA can be classified into antisense, Intergenic, fluorescent probe is bound to the lncRNA. Because
intronic, overlapping, bidirectional according to the lncRNA only express in transcriptional levelwithout protein
position and direction of transcription in relation to other expression, lncRNA FISH will be very important technique
genes, some companies set up lncRNA database with their to define the lncRNA expression within cells and tissues
primer designs for Q-rtPCR as Fig 3A. For example, though RNA FISH can be used to detect all three RNA
QIAGEN set up an in house database based on human (mRNA, miRNA and lncRNA) [8]. Some companies have
Gencode 19 with the confirmed lncRNA databases routinely serviced a probe design with their detection
containing over 28,000 RT of lncRNA qPCR Assays, their system.
RT2 lncRNA assays have increasingly used for
Fig 3: Clinical specific lncRNA technique. Alltechnologies to detect lncRNA are classified.
A. Q-rtPCR which have successfully employed in clinical fields;
B. lncRNA measurement by lncRNA FISH
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In microarray-based approaches as Fig 4A, two screening lncRNAs. Technically, after removal of rRNA from total
methods include traditional microarray and tiling array to RNA, which is suggestive, by some commercially available
identify lncRNAs. Because traditional microarrays can only kits, both polyadenylated RNA and non-polyadenylated
detect the presence or absence of known lncRNAs in an RNA can be used for lncRNA-seq. After sequencing, the
RNA pool, they cannot detect novel lncRNAs. DNA tiling generated reads are aligned to human hg19 reference
arrays contain oligonucleotide probes encompassing an genomes with TopHat software. The reads are used to
entire length of a defined DNA regionto identify novel assemble a transcriptome and discover previously
lncRNAs so that DNA tiling arrays are a major advantage un-annotated transcripts by Cufflinks. Novel lncRNAs can
to discover new lncRNA. Some companies developed their be identified by excluding protein-coding transcripts and
microarray chips to detect lncRNA such as Array star and annotated lncRNAs based on the databases of RefSeq,
Affymetrix with about 30,000 lncRNA expression panel ENCODE, and FANTOM (Functional Annotation of the
assay [9]. Mammalian Genome). Finally lncRNAs databases are
RNA-seq is a very powerful technique to detect and generated by either lncRNAdb or NRED (Noncoding RNA
quantify lncRNAs as Fig4B. Because disadvantage of a Expression Database) [10].
RNA-seq is the time and cost by the down stream analysis
of the data, it is only used to discover previously unknown
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lncRNAs Biomarkers for Tumor prediction proliferative, mesenchymal and differentiated), lung
As Table 2 demonstrated, RNA FISH techniques are squamal cell cancer (basal, classical, primitive and
increasingly used in lncRNA aberrant detection. For secretory), six type of prostate cancers. lncRNAs with
example, PCA3 and PCAT1 have been routinely studied in subtype-specific expression may have an important
relationship between prostate tumor and higher expression differences in individual subtypes. For example, MIAT
from lncRNA FISH for pathology diagnosis; GAS5 have showed specific expression in the mesenchymal subtype of
been reported in breast tumor. UCA1 is reported to ovarian cancer while RMST specially expressed in
down-regulated with bladder cancer [11]. Encouragingly, rhabdomyosarcoma. These lncRNA profiles are very
exon microarrays results support lncRNA FISH after study suggestive although these files should be further studied in
for thirteen different cancers because some of them have RNA FISH and Q-rtPCR to confirm these results regarding
been reported in prostate cancer, breast cancer andbladder cancer subtype.
cancer as lncRNA FISH results [12].
Because cancer is a clinically heterogeneous disease with
individual characteristics in different cancer subtypes,
Their microarray data further study subtypes of four can-
cers, for example, GBM (proneural, neural, classical and
mesenchymal), Ovarian Cancer (immunoreactive,
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PRP11-160H22.5, LOC149086,
Liver cancer plasma Up regulation
XLOC014172
Bladder cancer UCA1 Urine Up regulation
located in the SCNAs are related with tumorigenesis so that of lncRNAs through RNAi technology for LncRNA
they called a relationship as driver of tumorigenesis, or expression levels may be uncertain because of their
lncRNAs with SCNAs should result in corresponding gene secondary structure or intracellular localization. Its
expression changes [19]. These lncRNA between SCAN and potential application on patients is more limited as it
expression profiles are very suggestive although these involves targeted genetic manipulation [22]; (C) Structure
profiles should be further confirmed for cancer driver. disruption could be designed to bind to lncRNAs and
change or mimic their secondary structure. The targeting of
Clinical challenge for application harmful lncRNAs can be applied for gene therapy to
When the aberrant lncRNAs are discovered in tumor specific cellsbut some lncRNA has toxicity for normal cells
diseases, the aberrant detection will unfold a great chance [23]
. Although the potential application of lncRNAs is huge
for tumor diagnosis and therapeutic targets. LncRNAs can for therapeutic purpose, their complicated
be readily detected in biological fluids and their highly structures and functions should be further studied.
specific expression pattern can be assayed, and therefore It is indisputable that the clearer after we study lncRNA
lncRNAs could successfully be used for accurate function and structure, the more chances for clinical
diagnostics and classification. Although this application are scientists to apply for lncRNA into clinical diagnosis and
going to apply for circulating blood from clinical patients, treatment. Expectantly, lncRNA can approach our desire
the emerging techniques of circulating lncRNAs is which will fit lncRNA detection from laboratories into
restrained by the known information for tumor diagnosis, bedside patients for treatment of tumor disease.
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