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Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
- Source :
- Journal of Visualized Experiments : JoVE, Journal of visualized experiments : JoVE, Journal of visualized experiments : JoVE, JoVE, 2013, pp.e50713. ⟨10.3791/50713⟩
- Publication Year :
- 2013
- Publisher :
- MyJove Corporation, 2013.
-
Abstract
- International audience; The prostate-specific antigen (PSA) is the main diagnostic biomarker for prostate cancer in clinical use, but it lacks specificity and sensitivity, particularly in low dosage values 1. 'How to use PSA' remains a current issue, either for diagnosis as a gray zone corresponding to a concentration in serum of 2.5-10 ng/ml which does not allow a clear differentiation to be made between cancer and noncancer 2 or for patient follow-up as analysis of post-operative PSA kinetic parameters can pose considerable challenges for their practical application 3,4. Alternatively, noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease, e.g. PCA3 in prostate cancer 5,6 and to reveal uncharacterized aspects of tumor biology. Moreover, data from the ENCODE project published in 2012 showed that different RNA types cover about 62% of the genome. It also appears that the amount of transcriptional regulatory motifs is at least 4.5x higher than the one corresponding to protein-coding exons. Thus, long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) constitute a wide range of putative/candidate transcriptional regulatory sequences, as it is their primary function in infectious retroviruses. HERVs, which are spread throughout the human genome, originate from ancestral and independent infections within the germ line, followed by copy-paste propagation processes and leading to multicopy families occupying 8% of the human genome (note that exons span 2% of our genome). Some HERV loci still express proteins that have been associated with several pathologies including cancer 7-10. We have designed a high-density microarray, in Affymetrix format, aiming to optimally characterize individual HERV loci expression, in order to better understand whether they can be active, if they drive ncRNA transcription or modulate coding gene expression. This tool has been applied in the prostate cancer field (Figure 1).
- Subjects :
- Male
General Chemical Engineering
Endogenous retrovirus
Gene Expression
Genome
Transcriptome
0302 clinical medicine
Affymetrix
Diagnosis
RNA, Neoplasm
Tumor Markers
Cancer Biology
Oligonucleotide Array Sequence Analysis
MESH: Aged
Genetics
0303 health sciences
MESH: Middle Aged
General Neuroscience
Prostate
Middle Aged
prostate cancer
3. Good health
MESH: DNA, Single-Stranded
030220 oncology & carcinogenesis
Medicine
MESH: Biomarkers, Tumor
microarray
MESH: Endogenous Retroviruses
PCA3
DNA, Complementary
Human Endogenous Retroviruses
NcRNA transcription
DNA, Single-Stranded
[SDV.CAN]Life Sciences [q-bio]/Cancer
Biology
ENCODE
General Biochemistry, Genetics and Molecular Biology
03 medical and health sciences
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
[SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO]
Biomarkers, Tumor
Humans
Molecular Biology
030304 developmental biology
Aged
Prostatectomy
MESH: Humans
General Immunology and Microbiology
Microarray analysis techniques
Pharmacological
Endogenous Retroviruses
Prostatic Neoplasms
MESH: DNA, Complementary
MESH: RNA, Neoplasm
Biological
Microarray Analysis
MESH: Male
Retroviridae
MESH: Prostatic Neoplasms
MESH: Oligonucleotide Array Sequence Analysis
Human genome
Issue 81
HERV
Biomarkers
Subjects
Details
- Language :
- English
- ISSN :
- 1940087X
- Issue :
- 81
- Database :
- OpenAIRE
- Journal :
- Journal of Visualized Experiments : JoVE
- Accession number :
- edsair.doi.dedup.....d84631fc139a0c2bc909c37df1e70fed