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Experimental Therapeutics, Molecular Targets, and Chemical Biology |
1 The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute, 2 The Sidney Kimmel Comprehensive Cancer Center, and 3 Department of Molecular and Comparative Pathobiology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
Requests for reprints: Luis A. Diaz, Johns Hopkins Kimmel Comprehensive Cancer Center, 1650 Orleans Street, Cancer Research Building I, Room 590, Baltimore, MD 21231. Phone: 410-955-8878; Fax: 410-955-0548; E-mail: ldiaz1{at}jhmi.edu.
| Abstract |
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| Introduction |
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The major experimental problem with internal tumors is their quantitative assessment. Accordingly, many sophisticated methods have been devised to follow such tumors in mice. Direct imaging methods, such as magnetic resonance imaging or computed tomography, are useful in this regard but they can only detect relatively large tumors and require expensive equipment (8). Imaging with fluorescent or luminescent markers provides much greater sensitivity but also requires genetic engineering of the cell lines to introduce markers (9). The introduction of such markers can itself alter the growth characteristics of tumors (10). Moreover, direct or indirect imaging methods require that animals be anaesthetized and the imaging process takes a considerable amount of time. Imaging methods are therefore not well-suited for situations in which multiple sequential measurements on many mice are desirable.
In light of these problems, several studies have evaluated biochemical measurements ex vivo for internal tumor assessment. For example, tumor cells engineered to secrete human chorionic gonadotrophin can be monitored through the evaluation of the urine (11). Like the imaging methods noted above, this approach requires genetic engineering of each cell line to be evaluated. A more generally applicable approach is to use human DNA as a marker of tumor burden. Indeed, the concentration of human DNA sequences can be quantitatively assessed by real-time PCR and this principle has been applied to measure human tumor cells in the solid organs of mice, rats, and chickens (12–15). There has also been one recent report of the application of this approach to circulating DNA in mice harboring human ovarian xenografts (16). However, the DNA quantification method described in ref. 16 required the sacrifice of the mice to collect sufficient plasma for detection of human sequences. We have independently developed a facile approach that is more sensitive and allows repeated measurements from small amounts of plasma (<25 µL) collected from the tail veins of mice. As shown below, this technique can be effectively used to monitor the development of tumors in a variety of models and to track the efficacy of therapeutic measures.
| Materials and Methods |
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Subcutaneous and metastatic tumor models. Suspensions of 5 x 106 HCT116 parental cells in 0.1 mL of culture media were injected s.c. into the flank of mice. Tumors were measured with an electronic digital caliper (AVID) at the time indicated in the text. Tumor volume was calculated as length (L) x width2 (W) x 0.5. Metastatic models were established by injection of one million tumor cells in 500 µL of 1x PBS (HCT116) or 100 µL of McCoy's 5A medium (Cl-188) via the tail vein.
Orthotopic and ectopic tumor models. Tumor fragments were prepared via s.c. injection of 1 x 105 HCT116 or 143B cells in the flank of athymic nude mice. After subcutaneous tumors reached a size of 500 to 1,000 mm3, the mice were euthanized and the tumors were removed and placed in ice-cold 1x PBS (Invitrogen). For internal tumor implantation, athymic nude female mice were anesthetized with isoflurane (SurgiVet) and the abdomen was scrubbed for surgery. A small incision was made parallel to the linea alba and the cecum was exteriorized. A single fragment of tumor of
1 mm3 in size was implanted on the serosal surface. An absorbable suture (3–0 Vicryl) was used to attach the tumor to the serosal wall without penetrating the inner layers of the intestine. The organ was returned to the abdominal cavity, and the abdominal wall was closed. For transplantation to hepatic sites, an incision was made in the ventral left upper abdominal quadrant. The left lobe of the liver was carefully exposed and a blunt needle was used to puncture the liver capsule. A single fragment of tumor of
0.5 mm3 in size was then placed in the hole made by the needle. After hemostasis, the abdomen and skin were closed.
Plasma preparation. Whole venous blood was accessed by tail prick with a 26 1/2–gauge needle or scalpel blade and collected directly into a disposable EDTA-coated plastic capillary tube (Hematronics) or aspirated by pipette. Twenty-five microliters of whole blood was added to 200 µL of 1x PBS containing 4.5 mmol/L of EDTA (Invitrogen) in a 1.5 mL polypropylene tube (Corning Life Sciences) and subjected to centrifugation at 1,500 x g for 15 min at room temperature. Plasma was aliquoted and frozen at –80°C.
Human LINE quantification. DNA was purified from 100 µL of the diluted plasma samples using the QIAamp DNA micro kit (Qiagen) as recommended by the manufacturer with 1 µL of carrier RNA per 100 µL of AL buffer, eluted in 40 µL of EB buffer, and stored at –80°C. PCR was done in 25 µL with the following components: 13.75 µL sterile tissue culture grade double-distilled water (Invitrogen), 2.5 µL of 10x PCR buffer, 2.5 µL of 10 mmol/L deoxynucleotide triphosphates (U.S. Biochemical) 1.5 µL of DMSO (Sigma), 0.5 µL of SYBR Green I solution (Invitrogen) diluted 1:1,000 in double-distilled water, 0.5 µL of 50 µmol/L forward primer FWD 5'-TCACTCAAAGCCGCTCAACTAC-3' (Invitrogen; desalted, 25 nmol scale), 0.5 µL of 50 µmol/L reverse primer REV 5'-TCTGCCTTCATTTCGTTATGTACC-3' (Invitrogen; desalted, 25 nmol scale), 0.25 µL of Platinum taq DNA polymerase (Invitrogen), and 3 µL of purified DNA. The 10x PCR buffer contained 670 mmol/L of Tris-HCl (pH 8.8), 67 mmol/L of MgCl2, 166 mmol/L of (NH4)2SO4, and 100 mmol/L of 2-mercaptoethanol (18). Purified DNA from plasma was used directly without further dilution. The reaction was monitored on an iCycler (Bio-Rad) with the following cycling conditions: (94°C, 2 min) x 1, (94°C, 10 s; 67°C, 15 s; 70°C, 15 s) x 3, (94°C, 10 s; 64°C, 15 s; 70°C, 15 s) x 3, (94°C, 10 s; 61°C, 15 s; 70°C, 15 s) x 3, (94°C, 10 s; 59°C, 15 s; 70°C, 15 s) x 35. The threshold cycle number was determined using Bio-Rad analysis software (version 3.0.6070) with the PCR baseline subtracted. Various dilutions of normal human DNA purified from lymphocytes were incorporated in each plate to serve as standards. The numbers of mice per group are noted in the figure legends and all experiments were repeated at least twice with similar results.
Statistical analysis. Data are presented as mean ± SD. Student's t test (unpaired) was used as indicated in the text to compare continuous variables. The statistical significance level was set at P < 0.05.
| Results |
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100,000 of these elements exist in the human genome and, as shown below, a subset of these copies can be distinguished from mouse orthologues (19). The prototypical human LINE-1 consists of a 5' untranslated region (5'-UTR; nucleotide, 1–910), open reading frame (ORF) 1 (nucleotide, 911–1927), ORF2 (nucleotide, 1991–5818), and a 3'-UTR (nucleotide, 5819–6049) as depicted in Fig. 1A
. Using the BLAST algorithm (20), we found 81,587 matches of the canonical hLINE-1 (GenBank accession no. M80343) sequence in the human genome. Because members of the hLINE-1 family are known to be truncated (21), we generated a copy number map that allowed us to exclude regions with low abundance from primer design (Fig. 1B). The nucleotide start and stop positions for each entry were used to determine the presence of hLINE-1 subfragments among family members. For example, we found that the 5'-UTR was frequently truncated such that nucleotide positions 500 to 650 were only found in 6,253 (7.7%) of the 81,587 matches. On the other hand, the 3'-end of ORF2 (nucleotide positions, 5500–5650) was found within 36,936 hLINE-1 elements, representing 45.3% of all entries. Because hLINE-1 family members are divergent at the nucleotide level, we used the BLAT algorithm (22) to confirm the number of exact matches in the human genome for each candidate primer (data not shown) before they were tested empirically.
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The resultant assay was termed plasma LINE-1 optimized threshold (PLOT). Mouse plasma did not inhibit this assay when done as described in Materials and Methods, and the limit of detection was
0.06 pg of human DNA/µL plasma or
0.01 human cell genomes/µL of plasma. This limit was defined by PCR signals that arise at
25 to 27 cycles in plasma from mice without tumors, presumably due to background human DNA contamination. These background levels were consistent with the effective laboratory background of human DNA as defined by forensic criteria to be 0.0174 pg/µL with a range between 0.0119 and 0.0549 pg/µL (24).
Biological and technical issues. Studies in humans have shown that tumor DNA is often present in the plasma of cancer patients, particularly those with metastatic disease (25, 26). In such patients, the tumor DNA is generally degraded and amplicons of small size (
100 bases) are required for detection (27). We assumed that the plasma DNA from human xenografts would similarly be degraded. The primer set used for PLOT generated an 82 bp amplicon, allowing the detection of small circulating hLINE-1 DNA molecules. In the metastatic models described below, we found that this 82 bp hLINE-1 DNA fragment was
8- to 10-fold more highly represented in mouse plasma than a 150 bp fragment encompassing it, presumably due to degradation of the larger fragments in plasma. It is important to note that fragments of hLINE-1 are ubiquitous wherever humans are found. In the course of method development, we found that the maximum sensitivity of the assay was affected by the scale and source of primers. We compared primers from various commercial suppliers and found that the desalted, 25 nmol scale synthesis from Invitrogen yielded the least amount of contamination. In addition, every new batch of primer, as well as every component of the PCR mix, was carefully screened to ensure that it was not contaminated with human DNA.
PLOT in experimental models of malignancy. To determine whether hLINE-1 sequences could be detected in the plasma of mice bearing human tumor xenografts, we injected human colorectal cancer cells into the tail vein of athymic nude mice. The cell line chosen was an HCT116 derivative in which the wild-type PIK3CA allele was inactivated by targeted homologous integration. This cell line retained an endogenous mutant PIK3CA allele (arginine substituted for histidine at codon 1047) and metastasized widely when systemically injected into nude mice (17). The mice developed cachexia and metastatic deposits in a variety of target organs over 8 to 16 weeks (Fig. 2A
). Ten mice were injected with tumor cells and serial blood samples of 25 µL were taken from the tail vein. From these samples, the plasma fraction was collected, DNA was purified and the hLINE-1 content was measured by quantitative PCR (Fig. 2B). In tumor-bearing mice, hLINE-1 DNA became detectable in plasma 23 days after i.v. injection of cells. This was weeks before any animal developed tumors (Fig. 2A) or developed any other signs of illness. The quantity of hLINE-1 DNA increased with time and plateaued at
60 days following injection. The assay also provided a large dynamic range, apparent in Fig. 2B, with plasma hLINE-1 DNA increasing by >1,000-fold over the course of the experiment.
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5.5-fold between days 11 and 25, with growth slowing thereafter (Fig. 4A
). Plasma hLINE-1 DNA became detectable 10 days after injection, increased
5.8-fold between days 11 and 25, then plateaued (Fig. 4B). Note that tumor volume is only an approximate measure of viable tumor cells, as tumors contain necrotic regions, particularly as they reach large sizes, as well as nonneoplastic cells. Likewise, circulating DNA is only an approximate measure of tumor burden as it reflects dynamic states involving necrosis and apoptosis (29). Given these uncertainties, the data in Fig. 4 show a reasonable correlation between plasma hLINE-1 DNA and tumor bulk. Interestingly, plasma hLINE-1 DNA concentrations were considerably lower in mice with subcutaneous tumors compared with internal tumors (compare Fig. 4 with Figs. 2 and 3, noting the different scales for the Y-axis). This could be a result of the lack of invasiveness of subcutaneous compared with internal tumors. Alternatively, subcutaneous tumors may have fewer neoplastic cells per cross-sectional tumor burden than internal tumors, leading to less circulating tumor-specific DNA.
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PLOT as a biomarker for therapeutic response. The correlation between plasma hLINE-1 DNA and tumor burden and its rapid decline after tumor excision suggested that plasma hLINE-1 DNA might serve as a biomarker for nonsurgical forms of therapy. To test this possibility, we used an osteosarcoma cell line (OSTK) that had been modified to express thymidine kinase, thereby making it highly sensitive to ganciclovir. Tumor fragments from a subcutaneous xenograft of OSTK were implanted in the livers of athymic nude mice. The mice were then treated daily with ganciclovir or with vehicle alone on days 20 to 24. A potent therapeutic response was observed as hLINE-1 DNA levels in the treated group showed an initial increase followed by a decrease to below pretreatment levels by day 27. This pattern was not observed in the control group (Fig. 5A ). A linear plot from individual mice revealed a cumulative treatment-related spike in hLINE-1 DNA at day 23. This was present in all mice evaluated (one representative example is shown in Fig. 5B). On average, a 7.5-fold spike in plasma hLINE-1 DNA was noted in ganciclovir-treated mice, in contrast to mice treated with vehicle alone (P < 0.05, unpaired t test) where no such spike was observed. Dissection of mice following therapy confirmed the eradication of tumor in all treated mice and the persistence of tumor in control mice, with an average tumor volume of 3.19 ± 1.75 cm3 SD at necropsy.
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| Discussion |
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In aggregate, these studies suggest that the assay of circulating tumor-specific DNA will be generally useful for the study of human xenografts in cancer biology and drug discovery. The observations made in this manuscript, if extendable to humans, also suggest that circulating tumor DNA may be a surrogate marker for tumor burden and can be used to rapidly predict the efficacy of cytotoxic anticancer agents. Recent reports from our group and others show that tumor-specific mutations can be detected and quantified in the circulation of patients with metastatic colorectal cancers and melanomas (27, 31). Future studies using circulating tumor-specific DNA from preclinical models and patients with cancer will further define the utility of these biomarkers in cancer research.
| Acknowledgments |
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
The authors thank Evangeline (Latice) Watson for excellent technical assistance, the staff of the Cancer Research Building animal facilities of the Sidney Kimmel Cancer Center for assistance with animal experiments, and Nickolas Papadopoulos and Eike Gallmeier for critical review.
Received 2/13/07. Revised 6/14/07. Accepted 7/20/07.
| References |
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