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Other Original Studies |
Departments of Adult Oncology (R.C.T.A., P.L.M.D.) and Cancer Biology (P.L.M.D.), Dana-Farber Cancer Institute, and Departments of Genetics (G.C.) and Neurology (S.L.P.), Childrens Hospital, Harvard Medical School, Boston, Massachusetts 02115-6084
Address all correspondence and requests for reprints to: Patricia L. M. Dahia, Department of Cancer Biology/Adult Oncology, Dana-Farber Cancer Institute, 44 Binney Street, SM1010, Boston, Massachusetts 02115-6084. E-mail: patricia_dahia{at}dfci.harvard.edu
Abstract
Pheochromocytomas are neural crest-derived tumors that occur mostly
sporadically, but may also be part of inherited syndromes. The
molecular pathogenesis of sporadic pheochromocytomas remains unknown.
Recently, the susceptibility gene for familial paraganglioma syndrome,
a disorder embryologically related to pheochromocytomas, was
characterized and shown to encode the small subunit of succinate
dehydrogenase (SDHD), which is part of the mitochondrial complex II.
This complex regulates oxygen-sensing signals. Importantly, hypoxic
signals also appear to be related to the pathogenesis of
pheochromocytomas associated with von Hippel-Lindau syndrome. We
sequenced the entire coding region of the SDHD gene in a
series of pheochromocytomas. Although we did not find mutations in the
gene, we identified a new intronic single nucleotide polymorphism in
15% of the samples (g.97739A
G). We also confirmed the existence of
a sequence highly homologous to the SDHD complementary
DNA in chromosome 1p3436, a region commonly deleted in
pheochromocytomas. Full analysis of this sequence revealed a
heterozygous single base substitution in 70% of our samples that was
also present in the germline. This sequence does not appear to be
transcribed and is probably a processed pseudogene. Therefore, despite
its chromosomal location, it is unlikely that this sequence is a target
of loss of heterozygosity in pheochromocytomas. In conclusion,
mutations of the SDHD gene are not a common event in
this series of sporadic pheochromocytomas. The existence of
SDHD pseudogenes should be considered when analyzing
complementary DNA-based samples.
PHEOCHROMOCYTOMAS are rare neoplasms embryologically derived from the neural crest that occur mostly sporadically (1). In 10% of cases, pheochromocytomas are inherited as part of the multiple endocrine neoplasia type 2 syndrome (MEN 2A and 2B), von Hippel-Lindau (VHL) disease, and, rarely, neurofibromatosis type 1. Pheochromocytomas may also occur as an isolated familial form without other associated clinical features (2, 3). MEN 2A and MEN 2B are caused by germline mutations of the RET tyrosine kinase receptor (4), whereas VHL disease results from germline mutations of the VHL tumor suppressor gene (5). Somatic RET and VHL mutations are only rarely found in sporadic pheochromocytoma (6), suggesting that an additional gene(s) is involved in its pathogenesis.
Loss of heterozygosity (LOH) has been reported in several loci in pheochromocytomas: 1p3436, which affects 2570% of tumors (7, 8, 9, 10, 11); 3p2425, seen in 2040% of tumors (7, 9, 10); and 22q, which is seen in approximately 40% of the cases (7, 12). Less common sites of LOH in these tumors are 17p (7), 11q, and 11p (13). These loci might encompass a tumor suppressor gene(s) that may be involved in pheochromocytoma pathogenesis.
Nonchromaffin paragangliomas arising from the parasympathetic ganglia of the head and neck, in particular the carotid body (also known as chemodectomas), share a similar embryological origin with pheochromocytomas (14, 15, 16, 17). Recently, the SDHD gene was identified as a major susceptibility gene for the familial paraganglioma syndrome (PGL1), an autosomal dominant disorder with rare maternal transmission suggestive of imprinting (18). The SDHD gene encodes the succinate dehydrogenase subunit D gene (GenBank accession no. AB026906) representing the small subunit (cybS) of cytochrome b, which is a component of complex II of the mitochondrial respiratory chain (19). Mitochondrial complex II controls aerobic electron transport, which takes part on the regulation of oxygen sensing and signaling (20). It has been postulated that mutant cybS leads to cellular proliferation of paraganglionic tissue in response to chronic hypoxic stimulation resulting from its malfunction (18). Patients with PGL1 were found to have germline mutations of the SDHD gene, which are expected to disrupt the function of the protein, consistent with its role as a tumor suppressor. Nonsense and missense mutations were found in highly conserved regions of the SDHD gene in five PGL1 families (18). Despite its presumed maternal imprinting transmission, no evidence of germline imprinting of the SDHD gene was observed in the initially examined individuals.
The VHL protein has also been shown to be regulated by hypoxia (21). In the absence of functional VHL, a hypoxia-regulated transcription factor, hypoxia-inducible factor-1, is activated. As nonchromaffin paragangliomas are embryologically related to pheochromocytomas, and a hypoxia- mediated stimulus also appears to play a role in the pathogenesis of pheochromocytomas, in particular those associated with VHL syndrome, we tested the hypothesis that mutations in the SDHD gene are present in these tumors.
Materials and Methods
Samples
We studied 19 sporadic and 1 familial pheochromocytoma. Four of the sporadic tumors were malignant. Clinical data from the patients have been described previously (22). DNA from tumor and peripheral blood lymphocytes was prepared using standard protocols. Informed consent was obtained from all subjects and/or guardians involved in this study.
Ribonucleic acid was extracted from two pheochromocytomas using TRIzol (Life Technologies, Inc., Gaithersburg, MD), according to the manufacturers instructions and was reverse transcribed to complementary DNA (cDNA) with random primers, as previously described (23).
PCR, restriction digestions, and sequence analysis
Intronic primers flanking each one of the four SDHD
gene exons were designed based on the published SDHD genomic
sequence (GenBank accession no. AB026906) and were used for PCR (Table 1
and Fig. 1A
). Samples were subjected to 35 cycles
of 1 min each at 94, 58, and 72 C, followed by a final extension step
at 72 C for 10 min. PCR products were purified and sequenced as
previously described (24).
|
|
An additional forward primer (5F) was used in combination with the
SDHD/exon 4 reverse primer, 4R (Fig. 1A
and Table 1
), to
generate a 585-bp amplicon specific to an SDHD cDNA
homologous sequence located at chromosome 1p3436. This sequence will
be referred to hereafter as SDHDP1, in accordance with
nomenclature guidelines proposed by the HUGO gene nomenclature
committee (http://www.gene.
ucl.ac.uk/nomenclature/guidelines.html). The specificity of this
PCR is given by the forward primer (5F), which is unique to
SDHDP1. All pheochromocytomas were amplified, and the
products were purified and directly sequenced as above. Digestion of
this amplicon with AvaI (New England Biolabs, Inc.), according to the manufacturers guidelines, yields two
products of 302 and 283 bp.
RT-PCR
In addition to the primer combination above, another primer, 6F
(Table 1
), located downstream from 5F and mapping to the second exon of
the SDHD gene (Fig. 1A
), was used in combination with the 4R
primer to determine whether SDHDP1 was expressed in two
pheochromocytoma cDNAs. This primer combination would amplify a 416-bp
product from both SDHD and SDHDP1 sequences. To
ensure that the product generated was SDHD cDNA only and was
not a combination of SDHD and SDHDP1, this
resulting fragment was digested with AvaI (New England Biolabs, Inc.) according to the manufacturers guidelines. This
enzyme recognizes a single site in SDHDP1, generating
products of 302 and 114 bp, but does not cut the functional
SDHD gene.
Somatic cell hybrid mapping of the SDHD homologous sequence
To confirm the location of the SDHDP1 sequence, a
somatic cell hybrid panel generated using mouse and hamster backgrounds
(UK Human Genome Mapping Project-HGMP-Resource Center, Cambridge, UK)
was screened by PCR with primers specific to SDHDP1 (5F and
4R, Fig. 1A
), using the conditions described above. PCR products were
run on agarose gel, transferred to a nylon membrane, and hybridized to
an internal oligonucleotide (6F), as previously described
(25).
Results and Discussion
We did not find mutations of the SDHD gene in this
series of 20 pheochromocytomas. Two single nucleotide polymorphisms
were identified in the same 3 samples (15% of the cases): 1 is a novel
variant, g.97739A
G (according to the reference sequence numbering on
GenBank accession no. AB026906), and the other is c.204C
T (S68S),
which has been previously described (18). Both variants
could be distinguished by differential restriction digestion. The first
variant, identified by amplicon 3 and located 29 nucleotides upstream
of the start of exon 3, yielded 2 products of 223 and 70 bp after
digestion with TaqI (data not shown). The second variant was
previously identified and can be recognized by digestion with
SpeI, as described (18). One of the three
samples carrying both variants was from a malignant pheochromocytoma.
These variants were present in both tumor and germline DNA, suggesting
that they are probably polymorphisms. The frequency of the novel single
nucleotide polymorphism is similar to that seen in an equal number of
control chromosomes of an age- and ethnically matched population (data
not shown).
While searching the GenBank database, we identified a highly homologous
sequence of SDHD in 1p3436, a region known to show high
LOH rates in pheochromocytomas (7, 8, 10, 12). This
SDHD-like sequence had been found previously in a genomic
DNA library used to clone the SDHD gene (26).
This sequence, SDHDP1, differs from the SDHD
coding region at only six amino acids and maintains high homology
across the 3'-untranslated region (UTR; Fig. 1B
). However, the
homologous sequence lacks the SDHD introns and diverges from
SDHD in the 5'UTR, 13 bases upstream of the start codon.
This sequence has features compatible with a processed pseudogene,
i.e. it carries high homology with the cDNA sequence of a
functional gene without its introns, but is found integrated into a
distinct upstream context (27, 28, 29). Processed pseudogenes
represent a fraction of the pseudogenes present in the mammalian genome
and are believed to result mostly from retrotransposition followed by
random integration into the genome (27, 28, 29, 30). Based on the
GenBank annotation for this entry, SDHDP1 is located within
the third intron of the RH blood group CE (RHCE) locus (GenBank
accession no. AL031284) in chromosome 1p3536.13. By using a somatic
cell hybrid panel with primers designed to specifically recognize this
sequence, we confirmed the location of SDHDP1 to chromosome
1 (Fig. 2
).
|
T (numbered from the GenBank entry AL031284). This
nucleotide substitution would not result in amino acid change (aspartic
acid 113 in the original SDHD ORF). As this variation was
also present in germline DNA, this change was not a somatic event. No
other sequence variations of the SDHDP1 were seen in the
samples examined.
To determine whether SDHDP1 was transcribed, we used cDNA
from two sporadic pheochromocytomas as templates for PCRs. Using a
SDHDP1-specific forward primer (5F) in combination with the
reverse 4R primer, no product was amplified from cDNA; only genomic
templates amplified the expected 585-bp amplicon (Fig. 3
). To exclude the possibility that the
unique forward sequence was untranscribed, we also used a downstream
forward primer, 6F, which would recognize both SDHDP1 and
functional SDHD sequences in an RT-PCR. These two sequences
could be distinguished by differential restriction enzyme digestion, as
only SDHDP1 is cut by AvaI. We did not observe
any digested product from the pheochromocytoma cDNAs, which suggests
that SDHDP1 is either not transcribed or is transcribed at
very low levels in this tissue (Fig. 3
). Our findings, therefore,
suggest that this sequence is a processed pseudogene not expressed in
pheochromocytomas. The common sequence variation that we observed may
be the result of spontaneous mutation of the sequence that occurred
evolutionarily after the divergence between the functional gene and
SDHDP1. The existence of SDHD pseudogenes should
thus be considered when analyzing cDNA-based samples, as sequence
variations may confound the interpretation of the SDHD gene
mutation analysis.
|
Note Added in Proof
Since the submission of this manuscript, two other reports analyzed the role of SDHD in pheochromocytomas: Gimm et al. Cancer Res 2000; 60:6822-5 and Astuti et al.Lancet 2001; 357:1181-2.
Acknowledgments
We are grateful to Drs. Margaret Shipp, Charles Stiles, and Sérgio Toledo for their support, and to Dr. Charis Eng for her critical review of the manuscript.
Footnotes
1 This work was supported by NIH Grant -NS35701 and the Kyle
Mullarkey Research Fund (to S.P.), and NIH Grant P30-HD-18655 (to the
Mental Retardation Research Center Core DNA Sequencing Facility). ![]()
2 Special Fellow of the Leukemia and Lymphoma Society of
America. ![]()
3 These authors contributed equally to this work. ![]()
4 Recipient of a Susan G. Komen Breast Cancer Research Foundation
Fellowship (to C. Eng). ![]()
Received September 9, 2000.
Revised December 28, 2000.
Revised February 14, 2001.
Accepted February 28, 2001.
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