Computational Systems Biology Methods and Protocols.7z

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circulating tumor biomarkers. And in section 3 and 4, we will
introduce the ctDNA detection methods and its clinical
application.

2 Circulating Tumor Biomarkers


2.1 CTCs CTCs originate from the primary and metastatic tumor tissue.
Most CTC assays work by selecting tumor cells based on their
biological (protein expression) and physical properties (size, den-
sity, deformability, electric charge). Similar to ctDNA, CTCs have
been used to monitor tumor burden. CellSearch (Veridex, New
Jersey, USA) is an FDA-approved assay for the enumeration of
CTCs. Although commercially available, the clinical application is
limited due to low detection rates. Based on the characteristics of
CTC, it is applicable to assess the risk of progression after treat-
ment, rather than diagnosis before treatment [1]. Moreover, the
clinical value of CTC is limited to certain cancer types. For example,
CTCs can be detected in over 60% of patients with metastatic breast
and prostate cancer but only in 30–40% of patients with metastatic
colorectal cancer (mCRC) [2–4]. Compared with the CTCs
detected in metastatic breast and prostate cancer patients (median
6–7 CTC/7.5 mL), the CTCs detected in mCRC patients are
typically at a lower number (median 1–2 CTC/7.5 mL)
[5–7]. There are several reasons for this discrepancy. First, CRC
CTCs often travel in adherent clusters due to increased surface
adhesion molecules. Second, the circulation anatomy may affect
cell collection. Specifically, hepatic drainage of portal blood may
act as a filter, resulting in fewer CTCs in peripheral blood. Tumor
location also plays a role. For example, lower rectal tumors have
more CTCs in the central venous blood than tumors in the upper
rectum and colon. Finally, as CTCs undergo epithelial-
mesenchymal transition (EMT), cells lose their epithelial markers
and become more difficult to detect. CellSearch relies on the
expression of EpCAM, a marker of epithelial phenotype. Even
when the cells do express EpCAM, it has been shown that the
specific EpCAM antibody can greatly change the detection rate.


2.2 ctDNA ctDNA is comprised of fragments of tumor-derived cfDNA from
necrotic or apoptotic tumor cells. ctDNA can originate from CTCs,
metastases,or the primary tumor. Thereare two challenges in ctDNA
detection. First,a tumor-encoded somatic aberration(e.g., mutation,
translocation, or methylation event) must be present in the tumor
genome if it is ever to be detected in the blood. While genes such as
APC, TP53, and KRAS are frequently mutated in GI malignancies,
none is mutated in 100% of them. Second, the amount of ctDNA is
very likely related with tumor burden in a nonlinear manner. Small
amount of ctDNA is present in early-stage tumor, sometimes


46 Jun Li et al.

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