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598
Clinical Chemistry 42:4
598-603 (1996)
Denaturing gradient gel electrophoresis todiagnose multiple endocrine neoplasia type 2
ROBERT D. BLANK,l,2,3* CHARLES A. SKLAR,4 and MELISSA L. MARTIN2
Multiple endocrine neoplasia type 2 (MEN 2) is an autoso-
ma! dominant cancer syndrome caused by mutations in the
RET protooncogene. Others have already demonstrated the
value of genetic testing in known MEN 2 kindreds. Previ-
ously described approaches to DNA-level diagnosis, partic-ularly of index cases, are tedious. We developed appropriate
denaturing gradient gel electrophoresis (DGGE) condi-tions for analysis of exons 10, 11, and 16 of this gene, where
many of the pathogenic mutations map. We screened 16members of a three-generation MEN 2 kindred by DGGE
and found five affected but still asymptomatic patients,ranging in age from 5 to 67 years. We used DGGE to
localize the pathogenic mutations and screen at-risk indi-viduals in several other kindreds. DGGE-which requiresno radioactive, fluorescent, or chemiluminescent label-ing-is ideally suited to the diagnosis of MEN 2 because of
the syndrome’s dominant genetics and the rarity of clini-
cally silent variants in the RET gene.
INDEXING TERMS: neurocristopathy . thyroid neoplasms .
Hirschsprung disease #{149}mutational analysis
Multiple endocrine neoplasia type 2 (MEN 2) is a group of
autosomal dominant disorders that include familial medullarycarcinoma of the thyroid (MCT), MEN 2A, and MEN 2B.5
MEN 2 is characterized by hyperplasia of the calcitonin-secreting C cells of the thyroid [1]. These hyperplastic C cells
frequently undergo malignant transformation to MCT in af-
fected individuals. In familial MCT, no other tumors develop.
Division of Endocrinology, Departments of Medicine and ‘ Pediatrics,Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York. NY 10021.
2 Division of Endocrinology, Depamnent of Medicine, New York Hospital,
525 E. 68 St., New York, NY 10021.
‘Rockefeller University, Box 305, 1230 York Ave., New York, NY 10021.‘Mdress correspondence to this author, at Rockefeller University address. Fax
212-327-7420, e-mail rdblank’@mail.med.cornell.edu.
‘Nonstandard abbreviations: MEN 2, multiple endocrine neoplasia type 2;
MCT, medullary carcinoma of the thyroid; DGGE, denaturing gradient gel
electrophoresis; TBE, Tris-borate-EDTA; and SSCP, single-strand conforma-elonal polymorphism.
Received November 7, 1995; accepted January 15, 1996.
In the MEN 2A syndrome, pheochromocytomas and hyperpar-
athyroidism also develop in -50% and 20% of affected individ-
uals, respectively. In the MEN 2B syndrome, MCT and pheo-
chromocytomas develop in patients who have a characteristic
body habitus and multiple ganglioneuromata of both the entericnervous system and mixed peripheral nerves [2, 3].
Genetic tests for MEN 2 have recently been developed to
simplify the screening of individuals from affected kindreds
whose mutation is known. Most of these feature the use of
altered restriction sites to allow the detection of specific patho-
genic mutations in the RET protooncogene [4-7]. This ap-proach, while extremely useful when a restriction site is altered,
is limited by the fact that some pathogenic mutations do not
result in such an alteration [4]. Moreover, assessing new patients
for the presence of pathogenic RET mutations requires othermeans. Investigation of these individuals is a time-consuming
and labor-intensive task.
In this study, we report the development of denaturinggradient gel electrophoretic (DGGE) assays for exons 10, 11,
and 16 of the RET gene and demonstrate the utility of thismethod in diagnosing individuals in MEN 2 kindreds. Using
DGGE, we localized the RET mutations in the index case of a
new MEN 2B kindred and in a previously uncharacterizedkindred with familial MCT. We were also able to provide rapid
diagnosis of five asymptomatic members of a family with MEN
2A. We anticipate that DGGE methodology will greatly facili-tate the identification of familial disease among new index cases
of MCT.
Matenals and MethodsDNA extraction. Peripheral blood (5 mL) from each patient was
collected in EDTA-containing tubes, and the DNA was purifiedwith the QIAGEN (Chatsworth, CA) blood extraction kit as
recommended by the manufacturer. DNA was resuspended inTris-EDTA buffer (10 mmol/L Tris, pH 8.0, 1 mmol/L EDTA)
at a concentration of 50-200 mg/L and stored at 4 #{176}C.
PCR amplfication.PCR reactions were performed in 50-.tLvolumes in a Perkin-Elmer (Norwalk, CT) 480 thermal cycler.
All reactions were cycled (94 #{176}Cfor I mm, Tannealing for 1 mill,
72 #{176}Cfor 1 mm) for 35 cycles, followed by a 10-mm incubation
at 72 #{176}C.PCR primers, annealing temperatures, magnesium
Exon
10
11
13
16
ClampDouble clamp
mmol/L
1.5
1.0
1.5
1.5
1.0
Reference
8
8
This study
9
10
11
FinaI 6 bases of clamp omitted for this primer.5Sond step of two-step, heminested PCR for exon 11.
Clinical Chemistry 42, No. 4, 1996 599
Table 1. Primers and PCR conditions.
Primers t.,, #{176}C
GCGCCCCAGGAGGCTGAGTG 65
CGTGGTGGTCCCGGCCGCC
Clamp-CGTGGTGGTCCCGGCCGCC
CCTCTGCGGTGCCAAGCCTC 60
ClampaCCTCTGCGGTGCCAAGCCTC
CACCGGAAGAGGAGTAGCTG
Double clamp 60
GAGAAGAGGACAGCGGCTGC
CTCTCTGTCTGAACTtGGGC 65TCACCCTGCAGCAGGCCTtA
AGGGATAGGGCCTGGGCTC 60Clamp-AGGGATAGGGCCTGGGCTFC
TAACCTCCACCCCAAGAGAGCGCCCGCCGCGCCCCGCGCCCGTCCCGCCGCCCCCGCCGCGCCCCGCCCGCCCCGCGCGCGCCGCCCGCCGCGCCCCGCGCCCGTC
concentrations, and product lengths are listed in Table 1.Amplification reactions were carried out in 50 .tL of 10 mmol/L
Tris (pH 8.3 at room temperature) containing 50 mmol/L KG!,
0.1 g/L gelatin, 0.2 mmol/L of each dNTP, and 50 ng of DNA.
PCR products were purified from agarose gels with the QIAEX
(QIAGEN) gel extraction kit as recommended by the manufac-
turer.
Exon 11 products for DGGE were prepared in two rounds ofPCR: The first round used the clamped forward and unclamped
reverse primer designed by Donis-Keller et a!. [8]. Purified
product from this amplification was reamplified by using the
double-clamp primer and an internal reverse primer that lies 5’to a neutral polymorphism in this exon.
Restriction digests. Restriction endonucleases were purchased
from New England Biolabs (Beverly, MA) or Boehringer
Mannheim (Indianapolis, IN). Digestions were carried out in
20-pt volumes of the buffers supplied by the manufacturers.
Digests included 100-500 ng of purified PCR product and
0.5-2 U of enzyme. Incubations were for 2-16 h at 37 #{176}Cexcept
for BstUl, which was incubated at 60 #{176}C.
DNA sequencing. Direct sequencing of PCR products was carried
out with the Taquence (US Biochemicals, Cleveland, OH) kit
and use of 32P as recommended by the manufacturer. Electro-phoresis of sequencing ladders was carried out in 8% polyacryl-amide gels containing 7 mol/L urea with 1 x TBE buffer (89
mmol/L Tris, 89 mmol/L boric acid, and 2 mmol/L EDTA, pH8.3 at 25 #{176}G)at a constant power of 70 W.
DGGE. Gels were 8% polyacrylamide (acrylamide:bisacrylam-
ide 19:1 by wt.) in 0.5x TBE and were used within 3 h of
casting. DGGE was performed in a Bio-Rad (Hercules, CA)
Miniprotean apparatus at 45 V for 3-5 h. The 100% denaturant
was 7 mollL urea + 10 mol/L (40% by vol) formamide.
Intermediate denaturants were prepared by diluting 100% de-
naturant with 8% acrylamide in 0.5x TBE. In all experiments,
we used 1.5-mm spacers, which resulted in a gel volume of -9
mL. Gradients were prepared bottom-up by gravity flow in a
20-mL gradient maker with 5 mL of each acrylamide solution.
Details of the conditions used for each exon of RET are
summarized in Results. Samples were heated to 95 #{176}Cfor 5 mm
and allowed to cool to room temperature for 15 mm before
loading. Samples were visualized by staining in ethidium bro-
mide and using ultraviolet transillumination.
Results
We undertook DNA-level analysis of the RET gene in members
of known MEN 2 kindreds and in patients in whom the
existence of familial disease was uncertain. Because -90-95%[12] of the mutations causing MEN 2 had previously been found
in exons 10, 11, 13, and 16 of the RET gene [8, 10, 13-15], we
limited our analysis to these four exons. Full discussion of the
molecular and clinical features of MEN 2 in this patient
population will be presented elsewhere.
After extracting DNA from the peripheral blood from each
patient and at-risk individual, we carried out PCR amplification
and direct sequencing of the PCR products for each kindred’s
index case and for each sporadic patient. Both strands of thePCR products were sequenced. As we developed the DGGE
assays, we used these assays as the initial screen for their
respective exons. The presence and the absence of mutationswere confirmed by restriction digestion. Additional members of
known kindreds were screened by DGGE or restriction diges-
tion. We confirmed RET genotypes for all individuals by
repeating the genotyping with complementary methods.
DEVELOPMENT OF DGGE ASSAYS FOR RET GENE MUTATIONS
Because of the substantial effort required to seek mutations in
the RET gene by direct sequencing, we sought to develop a
reliable method with which we could find mutations more
rapidly. DGGE, which detects differences in the melting behav-
Fig. 2. Pedigree of family with C620R.
The arrow indicates the index case. Filling of symbols is as follows: upper left =medullary carcinoma of the thyroid, upper right = pheochromocytorna, lower left= hyperparathyroidism, and lower right = Hirschsprung disease. Note thataffected status is defined by clinical presentation at the time of genetic testing.not by the results of biochemical testing, so newly diagnosed cases are shownby open symbols.
600 Blank et a!.: DGGE to diagnose multiple endocrine neoplasia type 2
Fig. 1. DGGE assays for RET exons 10, 11,and 16.Lanes are numbered from left to right. (A) Exon 10:20-60% gradient run at 60 C. Lane 1, C620F;lane2, wild type; lane 3, C620R. (B) Exon 11:0-50% gradient run at 68 #{176}C.Lane 1, C634Y; lane2. wild type; lane 3, C634R. (C) Exon 16: 0-50%gradient run at 60 ‘C. Lane 1, M918T; lane 2. wildtype.
ior of PCR products as they migrate through a gradient of
formamide and urea in a polyacrylamide gel matrix [16], ap-
peared to be an appropriate technique for this use [11]. Because
affected individuals are heterozygotes, amplification of the
mutated exon of the RET gene, denaturation, and annealing will
result in four products: wild-type and mutant homoduplexes,
and two heteroduplexes (wild-type coding strand and mutant
coding strand). In particular, the heteroduplexes will have
nonhomologous “bubbles” present at the site of the mutation.
The bubbles in the heteroduplexes result in their having a lower
melting temperature than the homoduplexes. Consequently, an
affected individual will display two to four bands on DGGE, one
for each DNA species. In contrast, normal subjects will display
only a single band, as their PCR products contain only wild-type
homoduplex DNA. This difference in pattern is dramatic and
evident.
Thus far, we have found appropriate DGGE conditions for
the detection of mutations in exons 10, 11, and 16, as shown in
Fig. 1. We used the primer program [17] to estimate the melting
behavior of each PCR product by processively calculating the
annealing temperature of 20-hp windows. This analysis revealed
that residue 634 is contained within an unusually high melting-
point region of the RET gene. This fact required that we use a
61/62-base GG clamp and a higher gel temperature to detect
mutations at this site. We used a two-step amplification protocol
to incorporate this “double” GC clamp.
APPLICATION OF DGGE TO A THREE-GENERATION KINDRED
We used the exon 10 DGGE assay to test 16 members of a
family carrying the C620R mutation, as shown in Fig. 2. Five of
the individuals diagnosed with MEN 2 in this family were
asymptomatic on presentation; that is, they were first diagnosed
on the basis of the DGGE results. These results were in perfect
concordance with those obtained by BstUI digestion (data not
shown), which cleaves mutant but not wild-type exon 10. One of
these five asymptomatic individuals was in fact an obligate
affected individual, her son being clinically affected with
Hirschsprung disease and MCT.
Exclusion of disease is also important. Excluded individuals
need not undergo further assessment for the development of any
MEN 2-associated tumors, and their progeny are not at risk of
developing MEN 2.
DiscussionMOLECULAR PATHOLOGY OF THE RET GENE
The evidence is compelling that mutations of the RET protoon-
cogene cause MEN 2. Genetic studies had demonstrated that
the autosomal dominant locus causing MEN 2 was closely
linked to RET on chromosome lOq [18-20]. A limited set ofgermline mutations in RET have been found in -95% of MEN
2 kindreds, and several of these mutations have been found in
sporadic MCTs. Documentation of new RET mutations and denovo MEN 2 [21-23] also provides compelling evidence estab-
lishing RET mutation as the molecular lesion underlying MEN2. Most cases of MEN 2A and familial MTC are caused by
substitution of cysteine by another amino acid at one of five sites
near the transmembrane segment of the affected protein
[8, 15, 24, 25]. MEN 2B kindreds and one kindred with familial
MTC carry germline missense mutations at two sites withinRETs kinase domain [10, 13, 14, 20, 26]. Mutations at these
seven sites account for nearly all MEN 2 cases [12, 27].RET mutations also cause an autosomal dominant form of
Hirschsprung disease, in which a segment of bowel lacksinnervation; this presents clinically as intestinal obstruction in
infancy. Mutations in Hirschsprung disease span the entire RET
Clinical Chemistiy 42, No. 4, 1996 601
gene and include nonsense, frameshift, and deletion mutations
[9, 28-30]. Rarely, Hirschsprung disease and MEN 2A are both
present in a single kindred. These families have been found to
carry mutations characteristic of MEN 2A [31].
CLINICAL FEATURES OF MEN 2 AND SCREENING ISSUES
The tumors classified as MEN 2 may occur either as compo-nents of the syndrome or as sporadic neoplasms-and the
clinician must be able to distinguish between these. Various
features, including pathological findings and age of onset, help
to distinguish familial from sporadic disease but are far from
absolute criteria for doing so [32-36]. The increase of stimulated
calcitonin concentrations [37] is limited by age-dependent sen-
sitivity [34] and the occurrence of C cell hyperplasia in individ-
uals for reasons unrelated to MEN 2 [5, 38, 39].
Genetic methods overcome most limitations of the combined
use of clinical and biochemical methods for diagnosing MEN 2.
In the case of members of known MEN 2 kindreds, one must
determine only whether the pathogenic mutation is present in
the at-risk individual. A search for pathogenic mutations need be
performed only once for each kindred. Thus far, -95% offamilies with MEN 2 have had one of several characteristic
mutations in exon 10, 11, 13, or 16 of the RET gene. Availability
of an improved assay for these mutations would simplify genetic
diagnosis of the familial disease. We have achieved this by
establishing the conditions for DGGE of exons 10, 11, and 16.
DGGE COMPARED WITH OTHER APPROACHES TO GENETIC
DIAGNOSIS OF MEN 2
DGGE is ideally suited for diagnosis of MEN 2 for several
reasons. First, very few neutral polymorphisms are known in
these exons [40, 41]. Second, the dominant genetics of the
syndrome means that virtually all affected individuals are het-
erozygotes, which allows formation of heteroduplexes on PCR
amplification of DNA from affected individuals. The heterodu-plexes have early melting nonhomologous bubbles that are
readily apparent on DGGE. The presence of these heterodu-
plexes greatly simplifies the distinction of affected individuals,who display multiple bands on DGGE, from normal subjects,
who display a single band on DGGE. Moreover, DGGE does
not require the use of fluorescent, chemiluminescent, or radio-
active labeling for performance of the assay. These features,
together with the technical ease of performing an established
assay, make this an attractive method for use in clinical settings.
The sensitivity of DGGE in detecting single-base substitu-tions is -95% when performed with GC-clamping and PCRproducts <500 bp long [11]. Because the method cannot detectmutations in the highest melting temperature domain of the
molecule, GG-clamping introduces a high melting-point seg-
ment of DNA at the end of a PCR primer so as to placeamplified mutations in a context that maximizes their chance of
detection [16]. In the case of RET exon 11, the standard GC
clamp did not allow the detection of codon 634 mutations, but
these were revealed by extending the clamp length. In a recent
report, Attie et al. used DGGE of the RET gene to uncover a
7-bp deletion leading to Hirschsprung disease [28], but this
application required distinguishing between molecules that dif-
fered over the length of the microdeletion rather than at a single
base. Here, we have shown that DGGE with GC clamping is
sufficiently robust to detect the single-base substitutions that
result in MEN 2. Every RET mutation we have tested thus far
has been detectable by DGGE, and every individual tested has
had the results of DGGE confirmed by either restriction
digestion or sequencing of the PCR product. Two of our index
cases have had their status as MEN 2 patients established
initially by DGGE, one with the G620F mutation and another
with M918T.
A major limitation of DGGE is that neutral polymorphisms
will yield false-positive results. Thus, DGGE is inappropriate
for seeking exon 13 mutations, because the known pathogenic
mutation and a common neutral polymorphism [14, 41] occur at
consecutive residues in this exon; this mutation is a rare cause of
MEN 2, however. Another known polymorphism in exon 11
[40] of the RET gene is sufficiently distant from codon 634 that
a PCR product excluding the polymorphic site can be prepared
and analyzed.
Single-strand conformational polymorphism (SSCP) is an
alternative strategy for seeking mutations in defined regions of a
gene. SSCP conditions for all of the RET exons have recently
been published [41]. This method depends on the differencebetween the snap-back conformations of mutant and wild-type
DNA molecules subjected to heat denaturation and rapid cool-
ing. SSCP reportedly has a sensitivity of -80% and is easy to
perform. However, subtle differences in technique can have a
substantial impact on its results, and labeling of samples is
required [11]. Although DGGE conditions may be more diffi-cult to establish, once found, they are easily reproduced.
Alternative methods of mutation analysis are less attractive in
screening for MEN 2. Restriction digestion, chemical mismatchcleavage, and direct sequencing all require additional manipu-
lations after PCR and before electrophoretic analysis. Each
manipulation increases the opportunity for human error or
technical failure. In addition, some pathogenic mutations of
RET do not result in alteration of restriction sites. The accu-
mulation of heteroduplexes over the course of PCR amplifica-
tion results in reduced digestion, and distinguishing heterozy-
gosity from partial digestion is sometimes difficult. Finally,
restriction digestion is ill-suited to seeking mutations in new
index cases, because a large number of reactions must be used to
screen for all pathogenic mutations detectable by this approach.
In summary, we have developed DGGE assays for exons 10, 11,
and 16 of the RET gene. Mutations in these three exons arefound in >90% of MEN 2 cases. DGGE is particularly well
suited to the diagnosis of this syndrome because of the dominantgenetics involved and low prevalence of neutral polymorphism,
and because of the sensitivity and ease of performance and
interpretation of the assay. These tnethods allow detection of
most currently known pathogenic mutations in a simple, rapid
assay without the use of radioactive, fluorescent, or chemilumi-
nescent labels. They are suitable for both investigating members
of known kindreds and seeking pathogenic mutations in new
index cases.
602 Blank et a!.: DGGE to diagnose multiple endocrine neoplasia type 2
We thank the patients who participated in this study and their
physicians. Special thanks go to Julianne Imperato-McGinley,Murray Brennan, Jeffrey Friedman, and John Hall. This work
was supported in part by the Feer-Crawer Fund, Memorial
Sloan-Kettering Cancer Center. R.D.B. was supported by NIH
NRSA award F32-HG00084.
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