9 Aptamers for the Diagnosis of Malign Tumors
243
in the random DNA library as affinity reagents to capture target proteins. To avoid
the non-specific adsorption and cross-reactivity, SOMAscan assay employs a twostep continuous binding strategy. Every SOMAmer is functioned with a biotin, a
photocleavable group as well as a 5-position fluorescent tag before reacting with
the protein sample. Then, the formed SOMAmer-protein complexes are captured
using the streptavidin-coated beads, and then the protein is labeled with biotin.
After releasing the complexes through photocleavage, a common polyanionic dextran
sulfate compound is put into for nonspecific interaction desorption. Following the
recapture of the aptamer-protein complexes by the biotin through another set of beads,
the SOMAmers are isolated and then hybridize with complementary DNA probes of
a microarray chip. Finally, the concentration of SOMAmer can be reflected through
fluorescence intensity, which indirectly reflects target protein concentrations in the
initial protein sample. The major advantage of SOMAscan assay is that these slowoff-rates aptamers can bind corresponding target protein with significantly enhanced
force because of the chemical modification strategy [30]. These SOMAmers were
modified with hydrophobic moieties similar to their amino acid chains at the uridine,
which increases the chemical diversity and results in higher affinities. The binding
force is enhanced to a level similar to that between antibodies and antigens (Fig. 9.2).
The SOMAscan assays can finish more than one thousand proteins detection
simultaneously, and hundreds of samples per day, and only require relatively small
volumes of samples (at microliters level). The unique advantages of the SOMAscan
assay make it a powerful tool for the large-scale discovery of cancer biomarkers.
Gold et al. used the SOMAscan assay for chronic kidney disease (CKD) biomarkers
detection. Fifty-eight potential CKD biomarkers had been isolated from thousands
of patients’ plasma samples [28]. A large amount of disease biomarkers have been
identified by utilizing the SOMAmer-based assay from the blood-based samples
of various patients, such as malignant pleural mesothelioma, myocardial injury,
non-small cell lung cancer, and so on. Similarly, Baird et al used cerebrospinal
fluid (CSF) of patients and healthy people and identified 82 protein biomarkers
of Parkinson’s disease [31]. Recently, SOMAscan platform is applied to screen the
proteins from exosomes of prostate cancer, and more than 300 unknown proteins were
found as potential cancer biomarkers [32]. These studies indicate that the SOMAscan
technology has the potential to expand application in multiple disease biomarkers
discovery from different clinical biological samples.
9.3 Protein Biomarkers Analysis
Aptamers have been comprehensively involved in the development of protein
biomarker assay methods as the bio-recognition element for early cancer diagnosis,
due to their unique affinity with oncoproteins, cancer metabolites, and so on. The
conformational changes of aptamers after binding to their targets could be converted
into measurable signals. Several analysis methods are used such as electrochemical
243
in the random DNA library as affinity reagents to capture target proteins. To avoid
the non-specific adsorption and cross-reactivity, SOMAscan assay employs a twostep continuous binding strategy. Every SOMAmer is functioned with a biotin, a
photocleavable group as well as a 5-position fluorescent tag before reacting with
the protein sample. Then, the formed SOMAmer-protein complexes are captured
using the streptavidin-coated beads, and then the protein is labeled with biotin.
After releasing the complexes through photocleavage, a common polyanionic dextran
sulfate compound is put into for nonspecific interaction desorption. Following the
recapture of the aptamer-protein complexes by the biotin through another set of beads,
the SOMAmers are isolated and then hybridize with complementary DNA probes of
a microarray chip. Finally, the concentration of SOMAmer can be reflected through
fluorescence intensity, which indirectly reflects target protein concentrations in the
initial protein sample. The major advantage of SOMAscan assay is that these slowoff-rates aptamers can bind corresponding target protein with significantly enhanced
force because of the chemical modification strategy [30]. These SOMAmers were
modified with hydrophobic moieties similar to their amino acid chains at the uridine,
which increases the chemical diversity and results in higher affinities. The binding
force is enhanced to a level similar to that between antibodies and antigens (Fig. 9.2).
The SOMAscan assays can finish more than one thousand proteins detection
simultaneously, and hundreds of samples per day, and only require relatively small
volumes of samples (at microliters level). The unique advantages of the SOMAscan
assay make it a powerful tool for the large-scale discovery of cancer biomarkers.
Gold et al. used the SOMAscan assay for chronic kidney disease (CKD) biomarkers
detection. Fifty-eight potential CKD biomarkers had been isolated from thousands
of patients’ plasma samples [28]. A large amount of disease biomarkers have been
identified by utilizing the SOMAmer-based assay from the blood-based samples
of various patients, such as malignant pleural mesothelioma, myocardial injury,
non-small cell lung cancer, and so on. Similarly, Baird et al used cerebrospinal
fluid (CSF) of patients and healthy people and identified 82 protein biomarkers
of Parkinson’s disease [31]. Recently, SOMAscan platform is applied to screen the
proteins from exosomes of prostate cancer, and more than 300 unknown proteins were
found as potential cancer biomarkers [32]. These studies indicate that the SOMAscan
technology has the potential to expand application in multiple disease biomarkers
discovery from different clinical biological samples.
9.3 Protein Biomarkers Analysis
Aptamers have been comprehensively involved in the development of protein
biomarker assay methods as the bio-recognition element for early cancer diagnosis,
due to their unique affinity with oncoproteins, cancer metabolites, and so on. The
conformational changes of aptamers after binding to their targets could be converted
into measurable signals. Several analysis methods are used such as electrochemical