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RT-qPCR analysis of non-protein-coding RNA biomarker expression
RT-qPCR analysis of non-protein-coding RNA biomarker expression
Non-protein-coding
RNAs (ncRNAs) are expressed in viruses, archaea, prokaryotes and eukaryotes.
They fulfil vital roles in the regulation of chromatin architecture, epigenetic
memory, transcription, RNA splicing, editing and turnover [1, 2]. To date, at least
18 distinct types of ncRNA have been identified, which are classified according
to their size, function, subcellular localization and target specificity [3,
4].
A role for ncRNAs as biomarkers?
Any ncRNA that undergoes a quantifiable change in its expression profile, and
accompanies a change in cellular physiology or tissue homeostasis, is a
potential biomarker [5]. The challenge is to demonstrate a meaningful
association between the two. A growing body of literature suggests that
ncRNA expression is modulated in a variety of diseases and disorders
[4-11]. Indeed, ncRNA biomarker analysis is now in clinical use as a tool
to evaluate cancer risk, diagnosis and prognosis (Table 1).
Table 1 – ncRNA cancer biomarkers (adapted from [5]).
BIOMARKER |
ncRNA CLASS† |
TYPE OF CANCER |
LOCALIZATION |
UP / DOWN |
APPLICATION |
REF |
PCA3 |
lncRNA |
Prostate |
Tissue, Extracellular |
Up |
Diagnosis |
12 |
HULC |
lncRNA |
Pancreatic |
Tissue |
Up |
Prognosis |
13 |
HOTAIR |
lncRNA |
Nasopharyngeal |
Tissue |
Up |
Prognosis |
14 |
miR-21 |
miRNA |
Pancreatic
Glioblastoma and brain mets |
Tissue
Extracellular |
Down
Up |
Clinical outcome prediction, potential therapeutic target
Diagnosis
|
15
16 |
piR-651 |
piRNA |
Lymphoma
Gastric |
Tissue
Extracellular |
Down
Down |
Prognosis
Diagnosis |
17
18 |
SNORD33, SNORD66, SNORD76 |
snoRNA |
Non-small-cell lung |
Tissue, Extra-cellular |
Up Up |
Diagnosis Diagnosis |
19 |
piR-823 |
piwiRNA |
Gastric |
Extracellular |
Down |
Diagnosis |
18 |
miR-125a |
miRNA |
Oral |
Extracellular |
Down |
Diagnosis |
20 |
miR-200a |
miRNA |
Oral |
Extracellular |
Down |
Diagnosis |
20 |
miR-18a |
miRNA |
Liver |
Extracellular |
Up |
Diagnosis |
21 |
miR-221 |
miRNA |
Liver |
Extracellular |
Up |
Diagnosis |
21 |
miR-222 |
miRNA |
Liver |
Extracellular |
Up |
Diagnosis |
21 |
miR-224 |
miRNA |
Liver |
Extracellular |
Up |
Diagnosis |
21 |
miR-193b, miR-301, miR-131, miR-200b |
miRNA |
Non-small-cell lung |
Extracellular |
Up |
Diagnosis |
22 |
miR-10b |
miRNA |
Glioblastoma and brain metastasis |
Extracellular |
Up |
Diagnosis |
16 |
†lncRNA long non-coding RNA; miRNA microRNA; piRNA PIWI-interacting RNA; snoRNA small nucleolar RNA
Assays of ncRNA biomarker expression
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