Page 57 - Bio Engineering Approaches to Cancer Diagnosis and Treatment

3.3 Antibody-based microarray 55

not only facilitates more rapid marker discovery but also enables the direct obser-
vation of the relationships between proteins. Thus from single data sets, one could
examine a combination of multiple markers that may increase the statistical signifi-
cance of a diagnosis [33].
In an investigation of small intestine neuroendocrine tumors, Darmanis et al. have
used targeted bead arrays to investigate marker levels in plasma in two independent
study sets (77 and 132 samples, respectively) for 124 unique proteins. The classifica-
tion accuracy was up to 85%. They have used innovative biomarkers between the sig-
nificant panel to investigate them. Among these candidates, IGFBP2 and IGF1 were
indicated as new markers, thus the researchers have tested this through an ELISA
assay and subsequently have confirmed this indication [34].
Within the last decade among proteomic array techniques, antibody-based micro-
array has been the main technique in development and detection of new biomarkers
in cancer diagnosis. However, despite its advances and advantages (e.g., quality con-
trols, specificity, functionality, and/or reproducibility), this technique is not sufficient
alone and requires the input of other diagnostic techniques to complete validation.

3.3.1 PTM and its role in cancer diagnosis
One of the main reasons that antibody microarrays are a crucial technique in cancer
diagnosis is their ability to detect PTMs. A histone modification is a PTM of his-
tone proteins, which involves phosphorylation, acetylation, and methylation [35,36].
Phosphorylation, acetylation, and glycosylation activate signaling pathways and
change normal cellular function. Recent studies have shown that PTMs have a cru-
cial role in tumorigenesis and can provide useful information about the epigenetic
regulation of cellular processes. For example, modifications in cell surface receptors
such as receptor tyrosine kinases and G-protein coupled receptors can influence sig-
naling pathways and contribute to tumorigenesis. Phosphorylation is the best-charac-
terized modification in tumorigenesis. Until recent advances in antibody microarray
technology, the study of PTMs and their role in cancer diagnosis and prognosis had
been very limited.
Today, the role of phosphorylation in protein function is well characterized, with the
role of glycosylation, ubiquitination, and acetylation in tumorigenesis being intensely
investigated. During tumorigenesis, genetic alterations in signaling molecules lead to
the overactivation cell surface receptors, which consequently affects downstream sig-
naling pathways. For instance, membrane receptors, like HER2 and FGFR, and com-
ponents of the intracellular signaling cascade such as the K-RAS and ERK kinases,
could join and play abnormal signaling. PTM, like the phosphorylation of STY, causes
aberrant alternation and thus cells face to altered signaling. Recent investigations have
shown that genetic alterations, such as somatic or germline mutations, modulate the
functional activity of protein kinases (including multiple receptor tyrosine kinases and
phosphatases in the genome) which has a functional impact at the proteome level. In
summary, genomic alterations due to mutations functionally overactivated or alter sig-
naling pathways, which make cells susceptible to neoplastic growth.