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High-throughput mitochondrial genome screening method for nonmelanoma skin cancer using multiplexed temperature gradient capillary electrophoresis.

Many techniques have been developed to study genomic variation, including those based on electrophoretic conformational changes, enzymatic or chemical cleavage reactions, microarray analysis, heteroduplex detection, and HPLC fractionation. The goal of these screening techniques is to greatly reduce the need for DNA sequencing. This goal is easier to achieve when scoring a specific number of predetermined mutant alleles is the experimental objective rather than mutation discovery of unknown genomic variation, especially as the size of the genomic locus increases. Even DNA sequencing itself may not be dependable in some cases of heterozygosity, in cases of pooled specimens, or in cases of mitochondrial DNA (mtDNA) [1] heteroplasmy. DNA microarrays can be used to resequence entire genes or even smaller genomes on a single array, but this approach is not easily adaptable for the needs of many laboratories and remains costly. Currently, the gel-based assays offer an alternative for genomic variation screening but are limited in their capacity by the number of wells and available manpower.

Human mtDNA is a circular molecule consisting of 16 569 by encoding 2 ribosomal RNAs, 22 tRNAs, and 13 polypeptides involved in oxidative phosphorylation (1-3). Mutations in mtDNA can cause a variety of human diseases typically characterized by neurologic, muscular, or endocrine phenotypes. Recent publications reported a high frequency of homoplasmic mtDNA point mutations in a variety of human tumors (4-6). A possible explanation for mutant mtDNA homoplasmy in tumor cells is that mutant mtDNAs might alter mitochondrially mediated apoptotic pathways to escape cell death. Alternatively, the mtDNA changes may endow the tumor cell

Denaturing gradient gel electrophoresis (7), single-strand conformation polymorphism analysis (8, 9), conformation-sensitive gel electrophoresis (10, 11), thermal gradient gel electrophoresis (12), enzymatic cleavage (13-15), and denaturing HPLC (DHPLC) (16) are examples of presequencing screening methods that have been developed to detect DNA variants. DHPLC (17,18), oligonucleotide sequencing arrays (19), and temporal temperature gradient gel electrophoresis (TTGE) have been used successfully as screening tools for mtDNA mutations (20-24). In the case of denaturing gradient gel electrophoresis, single-strand conformational polymorphism analysis, and conformation-sensitive gel electrophoresis, the detection efficiency is ~80%. Some studies have reported that DHPLC has a sensitivity close to 100% when performed at the optimized temperature for each sample (25). However, melting domains must be precisely determined, and DNA molecules with multiple melting domains may need to be run on the column at multiple temperatures. In addition, DHPLC has a throughput limited by the serial nature of injecting DNA samples onto a single column, although this technique can be amenable to multiplexed assays (17, 26).

Temperature gradient capillary electrophoresis (TGCE) is a high-throughput method for detection of DNA variation with a high sensitivity, rapid separation time, and a small DNA concentration (~200 pg/ [micro]L) requirement (27). TGCE identifies DNA variations in ethidium bromide-stained heteroduplex strands by use of capillary gel electrophoresis in a parallel array run through a programmable thermal gradient in combination with a laser-induced fluorescence detection system (28, 29). We report the application of this new high-throughput method for detection of mtDNA sequence variations in cutaneous tumors and the first use of multiplexed TGCE mutation detection without the requirement for fluorescently tagged DNAs.

Materials and Methods

PATIENT POPULATION AND COLLECTION OF CLINICAL SKIN SAMPLES

Skin was obtained from patients with nonmelanoma skin cancer (NMSC) undergoing skin cancer excision by Mohs micrographic surgery in our Dermatology Clinic. Samples were collected under a protocol approved by the Vanderbilt University Institutional Review Board.

DNA ISOLATION AND PCR

Genomic DNA was isolated from squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) samples by use of the DNeasy Tissue Kit (Qiagen Inc.). DNA from four tumor samples (two SCC and two BCC) was screened with use of 17 overlapping PCR amplicons. Oligonucleotide primers (Sigma Genosys) were used for amplification of the entire mtDNA (Table 1). The PCR amplicons were visualized by gel electrophoresis on a 1% agarose gel stained with ethidium bromide. Reactions were performed in a 50-[micro]L volume containing 10 ng of total genomic DNA as template, 0.2 mM each deoxynucleotide triphosphate (New England BioLabs), 0.5 [micro]M each of the forward and reverse primers, and 2.5 U of Optimase polymerase (Transgenomic Company) in 1 x Optimase [Mg.sup.2+]-free buffer supplemented with 1.5 mM magnesium sulfate. PCR conditions for all amplicons were 30 cycles of 95[degrees]C for 30 s, 60[degrees]C for 1 min, and 72[degrees]C for 2 min, followed by cooling to 4[degrees]C. The initial denaturation was at 95[degrees]C for 5 min, and the final elongation was at 72[degrees]C for 5 min.

DIGESTION OF AMPLICONS

For multiplex analysis, PCR products were digested with restriction endonucleases (Table 1 in the Data Supplement that accompanies the online version of this article at http://www.clinchem.org/content/vol51/issue2/). The digestions using DpnII, DdeI, MspI, AluI, and HaeIII (New England BioLabs) were performed in Optimase buffer at 37[degrees]C for 2 h in a total volume of 25 [micro]L. Results of these digestions were visualized by gel electrophoresis on a 2% agarose gel stained with ethidium bromide.

SAMPLE PREPARATION FOR TGCE

Our intended use of this screening technique is for the detection of somatic mtDNA mutations in tumors. However, for the purpose of validating this method, we allowed heteroduplex species to form by mixing the tumor DNA with our laboratory reference DNA isolated from the skin of a healthy 30-year-old volunteer in a 1:1 ratio. The samples were denatured for 3 min at 95[degrees]C and annealed in a thermal cycler via a stepwise reduction in temperature as follows: decrease from 95[degrees]C to 80[degrees]C at 3[degrees]C/min, decrease from 80[degrees]C to 55[degrees]C at 1[degrees]C/min, hold at 55[degrees]C for 20 min, decrease from 55[degrees]C to 45[degrees]C at 1[degrees]C /min, and decrease from 45[degrees]C to 25[degrees]C at 2[degrees]C /min. Samples were stored at 4[degrees]C until TGCE analysis was performed.

TGCE analysis was performed on a Reveal Discovery System (SpectruMedix). This system performs temperature gradient electrophoresis for DNA variant detection on an automated 96-capillary array instrument. DNA samples consisting of homoduplexes and heteroduplexes were separated by capillary electrophoresis, during which a thermal ramp from 50[degrees]C to 60[degrees]C was applied over 25 min. The injection conditions were 6 kV for 90 s, and the capillary length was 70 cm. The gel in the capillary was 20 g/L 7 x [10.sup.6] molecular weight polyethylene oxide dissolved in 1 x Tris-borate-EDTA buffer with ethidium bromide added at a final concentration of 0.5 mg/L. SpectruMedix Check Mate Software was used for instrument control and data acquisition with a data acquisition time of 65 min. Data were analyzed by use of the SpectruMedix Reveal Mutation Software, which generated mutation scoring results for all samples in a 96-well tray. The system generated the electropherograms for our reference sequence, the wild-type plus mutant (mixed) samples, and the mutant unmixed samples. Mutations were identified by automated detection of peak patterns where the presence of two peaks on an electropherogram indicated a nucleotide change. All mutant DNA sequences were confirmed by use of the ABI 377 automated DNA sequencer (Applied Biosystems) in the Vanderbilt

DNA sequencing core laboratory. Results

Oligonucleotide primers were designed to amplify the entire mitochondrial genome in 17 amplicons at a single annealing temperature and with a mean amplicon size of 1.1 kb (range, 418-2002 bp; Table 1 in the online Data Supplement). mtDNA from four NMSC patients with known nucleotide changes previously identified by sequencing was screened by TGCE. Samples were prepared for singlet or multiplexed TGCE by restriction enzyme digestions (Table 1). The targets for detection were in 20 NMSC mtDNA variants: 8 from BCC and 12 from SCC tumors (Table 1).

The corresponding mixed (tumor plus control), control, and tumor DNAs are shown in the electropherograms designated with letters M, C, and T, respectively, in Figs. 1 and 2 of the online Data Supplement. Amplicon length is given in parentheses for each panel. Single peaks are expected in homoduplex species, whereas multiple peaks are expected in heteroduplex species. Examples of the TGCE output showing the detection of heteroduplexes in mixed specimens are presented in Figs. 1, 2, and 3 and are displayed in tabular format in Table 1. Fig. 1 shows examples of the successful detection of the T5004C, G9123A, and A15326G mutations from SCC tumors and A9448G, A13032G, and A16051G mutations from BCC tumors. In this analysis, the sensitivity was 70% (14 of 20) for the detection of these mutations in singlet reactions despite the generally large sizes of the amplicons.

For multiplexed analysis, each large PCR product (0.8-2 kb; Fig. 3 in the online Data Supplement) was digested with the appropriate restriction enzyme (Table 1 in the online Data Supplement) to generate smaller fragments that could be individually resolved by TGCE (Fig. 4 in the online Data Supplement). DNA digests from amplicons 5, 6, 11, 12, and 15 generated DNA fragments <50 bp, which are not analyzable in our assay because DNA oligonucleotide primers are not removed before TGCE loading. These small fragments are generated at the ends of the amplicons, and the regions containing these smaller fragments are screened by larger adjacent overlapping amplicons. Examples of successful multiplexed screening for amplicon fragment 11 (digested with DdeI to generate three analyzable products of 187, 198, and 390 bp) are shown in Fig. 2A. As shown in the electropherogram in Fig. 2A, the G9123A mutation was detected in the 390-bp digestion product of the mtDNA of SCC tumor S3T. Fig. 2B shows the electropherogram produced by multiplexed TGCE analysis of fragment 17. AluI digestion of the 1029-bp amplicon from BCC tumor specimen B8T yielded fragments of 218, 352, and 459 bp, which were resolved by TGCE, and enabled successful detection of the A16051G mtDNA mutation in the 459-bp fragment (Fig. 2B).

A 2002-bp amplicon was the largest fragment analyzed in singlet and multiplexed reactions. Two mutations were detected by multiplexed analysis in tumor specimens S3T and S2T in this region of the mtDNA, and one of these two mutations (C10527T in 52T) was also detected in a singlet reaction despite the large amplicon size. Fig. 3A shows an electropherogram for the successful detection of the C10527T mutation in a uniplex reaction from fragment 12 of SCC tumor specimen 52T. The results of multiplexed analysis of the same fragment are shown in Fig. 3B. Digestion with Alul generated five analyzable products of 247, 312, 366, 440, and 588 by and two nonanalyzable products of 12 and 17 bp. An extra peak representing a heteroduplex species is present in the 588-bp fragment and corresponds to the location of the C10527T mutation.

[FIGURE 1 OMITTED]

Both heteroplasmic and homoplasmic mtDNA mutations were detected in these experiments (Table 1). The application of multiplexing by digestion of the larger amplicons with restriction endonucleases improved the sensitivity of the approach. Analysis of smaller DNA fragments improved the overall sensitivity of the approach to 90% (18 of 20 mutations detected). There were no false positives identified in this TGCE protocol when the Optimase DNA polymerase was used for amplification of the PCR products.

Discussion

Detection of DNA variations has become a focus in many areas of genetics, particularly in the study of genes associated with human disease. For mutation screening of a limited number of specific alleles, assays such as sequencing, real-time PCR with molecular beacons, and pyrosequencing have advantages, including automation and high-throughput capabilities in a properly equipped laboratory. The task of screening DNA sequences for unknown mutations or sequence variations is considerably more complex. Although sequencing and DNA microarray chips are capable of generating these data, they generate enormous amounts of data at a high cost. Gel-based screening techniques are often more cost-effective and certainly diminish the need for sequencing, but gel-based methods are limited in their potential through-put. Two techniques have emerged that combine high-sensitivity heteroduplex detection with automated liquid handling for the process of mutation discovery: DHPLC and TGCE.

[FIGURE 2 OMITTED]

In our study, we evaluated the use of TGCE to screen for the presence of mtDNA sequence variations in human NMSC samples. We developed a set of 17 oligonucleotide primers to amplify the entire mitochondrial genome in overlapping segments by PCR using a single annealing temperature. The amplicons were then digested with restriction endonucleases to generate a series of smaller fragments with sizes sufficiently different to allow for multiplexed TGCE analysis without an additional need to fluorescently label each product to be resolved in the capillary. The use of the smaller DNA fragments generated by the multiplexing also improved the sensitivity of the approach over uniplex reactions with larger amplicons. Like other heteroduplex detection methods, the amplified DNA must be mixed with control DNA, and the combined sample must be denatured and cooled slowly to allow for the formation of heteroduplexes. Mixing with a control DNA is not always necessary if screening for only heteroplasmic mutations is desired. We have performed TGCE analysis with serial dilutions of samples with known mtDNA mutations to determine the sensitivity of TGCE in detecting low degrees of heteroplasmy. We have observed successful mutation detection when the altered base is present in concentrations as low as 10% of the total mtDNA species (data not shown). TGCE was also particularly amenable to multiplexing because the programmable thermal gradient allows for the analysis of DNA variations in multiple thermal domains. Indeed, a single reaction condition was capable of detecting 90% of our previously known mtDNA sequence variations in these tumors. The mtDNA has an overall GC content of 44.3%. The two amplicons with mutations that were not detected under these TGCE conditions had GC contents of 47.1% and 47.7%, respectively, and were among the four amplicons with the highest GC content. It may be possible to achieve even better results with refinement of the thermal gradient conditions, such as use of a narrower temperature ramp (27) or with the use of techniques such as the addition of a GC clamp to the end of the amplicons to change the melting profiles.

A variety of methods for mtDNA mutation screening have been published, such as DHPLC (17) and TTGE (20). TGCE in the 96- or 384-well format offers substantial advantages over these techniques in terms of sample capability, which is limited by the number of wells and manual gel preparation for TTGE and by the serial nature of running DNA on a DHPLC column. Furthermore, the melting profiles of the DNA fragments generated by multiplexed assays often require multiple injections on the DHPLC column at various temperatures to ensure optimum sensitivity, which further limits the maximum capacity of the system. With TGCE, the throughput of the device is limited by the number of capillaries in the array. However, the parallel nature of the analysis combined with a short running time and automated plate handling makes the maximum throughput higher than existing methods for mtDNA mutation screening. In terms of the sensitivity and cost, TGCE required low sample concentrations and has a relatively low cost for sample preparation because the unpurified PCR product is used to perform the analysis. This screening method could be useful for detecting inherited germline mutations in mtDNA in patients with mitochondrial disease or to detect acquired somatic mutations of mtDNA. The sensitivity of the assay could also be useful in population studies using pooled mtDNA. The limitations of this procedure are its inability to distinguish between mutant and wild-type homoduplexes without mixing and the lack of separation of multiple distinct heteroduplexes species such as can been seen in DHPLC or TTGE. As in other heteroduplex-based mutation detection methods, incomplete restriction enzyme digestion may interfere with the detection of DNA variants, and small restriction fragments may be lost. Furthermore, detection of unknown mtDNA mutations still requires sequencing in the region to identify the specific nucleotide change. In conclusion, we found that TGCE could be a useful tool for mutation discovery in mtDNA and also offers several advantages over existing methodologies. TGCE combines high-sensitivity heteroduplex detection with high-throughput capability. This screening method was 90% sensitive and 100% specific in our assay to detect predetermined mtDNA mutations. The system offers high flexibility for multiplexing (without a need for additional fluorescent tagging of DNA) and mutation detection in a broad range of DNA melting domains. This method could facilitate the rapid detection of mtDNA sequence variations and be applicable to wide variety of mutation discovery applications.

[FIGURE 3 OMITTED]

This work was supported by a VA Medical Research Service Advanced Career Development Award, by a Vanderbilt Skin Diseases Research Center Pilot and Feasibility Award (NIH P30AR41943), by an American Cancer Society Institutional Research Grant, and by an Ellison Medical Foundation New Scholar Award to Dr. Sligh. We thank Drs. Michel McDonald and Thomas Stasko for generously providing patient materials.

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[1] Nonstandard abbreviations: mtDNA, mitochondrial DNA; DHPLC, denaturing HPLC; TTGE, temporal temperature gradient gel electrophoresis; TGCE, temperature gradient capillary electrophoresis; NMSC, nonmelanoma skin cancer; SCC, squamous cell carcinoma; and BCC, basal cell carcinoma. with a selective growth advantage directly or in combination with acquired nuclear-encoded mutations.

WILLIE GIRALD-ROSA, [1,2] RUTH A. VLEUGELS, [1,2] AMY C. MUSIEK, [1,2] and JAMES E. SLIGH [1,2,3] *

[1] VA Tennessee Valley Healthcare System, [2] Department of Medicine, Division of Dermatology, and [3] Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN.

* Address correspondence to this author at: Vanderbilt University Medical Center, Division of Dermatology, A2303 Medical Center North, Nashville, TN 37232-2600. Fax 615-343-4365; e-mail james.sligh@vanderbilt.edu.

Received July 16, 2004; accepted November 18, 2004.

Previously published online at DOI: 10.1373/clinchem.2004.040311
Table 1. Detection of mtDNA variations by TGCE in NMSC tumors.

 Nucleotide
Tumor Amplicon no. change Gene

B1T 5 G3010A RNR2
B1T 7 A4769G ND2
B1T 11 A9448G CO3
B1T 16 A15326G Cyt-b
S2T 3 C476T RNR1
S2T 8 G5979A CO1
S2T 10 C7956T CO2
S2T 12 C10527T ND4L
S2T 13 C12465T ND5
S2T 1 C16520T D-loop
B8T 2 A263G R sequence
B8T 14 A13032G ND5
B8T 16 C15409T Cyt-b
B8T 17 A16051G D-loop
S3T 6 C3992T ND1
S3T 7 T5004C ND2
S3T 10 G8269A CO2
S3T 11 G9123A ATP6
S3T 12 A10044G tG
S3T 16 A15326G Cyt-b

 Detected in Detected in Homoplasmy or
Tumor uniplex? multiplex? Heteroplasmy

B1T No No
B1T Yes Yes Homoplasmy
B1T Yes Yes Homoplasmy
B1T No Yes Homoplasmy
S2T Yes Yes Homoplasmy
S2T No No
S2T Yes Yes Heteroplasmy
S2T Yes Yes Homoplasmy
S2T No Yes Homoplasmy
S2T Yes NAa Heteroplasmy
B8T Yes NA Homoplasmy
B8T Yes ND Homoplasmy
B8T No Yes Homoplasmy
B8T Yes Yes Homoplasmy
S3T Yes Yes Homoplasmy
S3T Yes Yes Homoplasmy
S3T Yes ND Homoplasmy
S3T Yes Yes Homoplasmy
S3T No Yes Homoplasmy
S3T Yes ND Homoplasmy

(a) NA, not applicable (no multiplex analysis for small
fragments); ND, not done.
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Title Annotation:Molecular Diagnostics and Genetics
Author:Girald-Rosa, Willie; Vleugels, Ruth A.; Musiek, Amy C.; Sligh, James E.
Publication:Clinical Chemistry
Date:Feb 1, 2005
Words:4044
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