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Transcript
[CANCER RESEARCH54, 6321—6324,
December 15, 1994]
Advances
in Brief
CDKN2 (p16/MTS1) Gene Deletion or CDK4 Amplification Occurs
in the Majority of Glioblastomast
Esther
E. Schmidt,2
institute for Oncology
Stockholm, Sweden
Koichi
and Pathology,
Ichimura,2
Division
Guido Reifenberger,
of Tumor Pathology,
and V. Peter Collins3
and Ludwig
institute for
Abstract
Forty-six gioblastomas,
16 anaplastic astrocytomas,
and 8 astrocyto
mas were studied for the loss of the CDKN2 (p16/MTSJ) gene on 9p. The
CDKN2 locus was homozygously deleted in 19 of 46 glioblastomas (41%)
and 1 allele was lost in an additional 13 cases (28%). The deleted regions
were limited centromerically in some cases by the MTS2 locus and tab
merically by the 1063.7 locus. CDKN2 was homozygously
deleted in 3 of 16
anaplastic astrocytomas (19%) and 2 further cases showed loss of 1 allele.
Amplification of the CDK4 gene was present in 7 of 14 (50%) glioblasto
mas and 3 of 11 (27%) anaplastic
astrocytomas
Cancer
Research,
Stockholm
Branch,
Karolinska
Hospital,
S-171
76
In this study we have carried out an allelic assessment at the
CDKN2, MTS2, and surrounding loci in a series of 70 human glioma
tissue samples. The findings support a role for the CDKN2 gene as a
tumor suppressor gene in glioblastomas and anaplastic astrocytomas;
furthermore we have found that CDK4 gene amplification is a com
mon abnormality in tumors not showing loss of CDKN2 gene alleles.
It would appear that aberrations of the genes coding for components
of this cell cycle-regulatory system occur in at least 85% of human
glioblastomas and 50% of anaplastic astrocytomas.
with no losses at the
CDKN2 locus as well as in 2 of 32 (6%) glioblastomas with CDKN2 losses.
Thus one or more of these two genes were shown to be aberrant in 85%
of glioblastomas and 50% of anaplastic astrocytomas. None of the 8
astrocytomas showed abnormalities of these genes.
Materials
and Methods
Tumor
Material,
8 astrocytomas
reported
Cytogenetic and molecular genetic analyses of anaplastic astro
cytomas and glioblastomas [WHO malignancy grades III and IV
(1)] indicate consistent loss and amplification of genetic informa
tion at several specific genomic locations (2—6).One region of loss
found among anaplastic astrocytomas and glioblastomas involves
portions of the short arm of chromosome 9. The common region of
homozygous deletion has been defined as lying between the
were included
previously
extraction,
Introduction
DNA Extraction,
and Southern
Blotting Analysis.
A
total of 70 tumors including 46 glioblastomas, 16 anaplastic astrocytomas, and
in this study. Almost
(constant
case
number)
Southern blotting, hybridization,
all of the cases have been
in various
studies
(4, 6). DNA
exposure on Storage Phosphor
Screens, and analysis using a Phosphorlmager (Molecular Dynamics, Sunny
vale, CA) and ImageQuant software were performed as described (4). For
Southern blotting, TaqI was used as the restriction enzyme.
DNA Probes. DNA probes were generatedby PCR amplificationusing
the following
primers
CDKN2(MTSJ)
(exon
and
normal
human
leukocyte
DNA
as template:
1) (2FU, CCCAGTCACGACGTfGTAAAACGACG
GCCAGTGAAGAAAGAGGA0000CFG;
1108R, GCGCTACCFGAUC
CAATFC); CDKN2(MTSJ)(exon 2)(42F, GGAAATFGGAAACTGGAAGC;
551RU, CCCAGTCACGACGrFGTAAAACGACGGCCArFCTGAGCrF
TGGAAGCFCF);
MTS2 (89F, TGAG1TFAACCFGAAGGTGG;
50R, GGG
D9S171locusandtheIFNce/wgenecluster(4). Thisregionhas TGGGAAATTGGGTAAG);1063.7 (forward, CCG1TFCAGCTTCTCAT
been reported
to be deleted in various tumors suggesting
that a
CAC; reverse,CCGACFGTCCCAUGTGAU); cl.b (forward,AAGCITF
tumor suppressor gene common to different malignancies is local
CCCACAAACFGGC;
ized in this limited area. Recently, the CDKN2 (p16/MTSJ) gene
was identified in this area and shown to be deleted in a series of
cell lines (7—9).The CDKN2 gene has been reported to be mutated
in some families with inherited melanoma susceptibility (10, 11)
and also in a high proportion of esophageal (12), pancreatic (13),
and non-small cell lung carcinomas (14).
p16 has been shown to specifically inhibit the binding of the CDK4
protein to cyclin Dl (9). Cyclin Dl and CDK4 form a complex which,
among others, is capable of phosphorylating the Rbl protein and thus
p16 is involved in inhibiting cells progressing from G1 into S phase.
The MTS2 gene has recently been reported to code for a protein,
p15Thl@(4B,
which has a similar function (15). We have previously
described amplification of the CDK4 gene in approximately 15% of
anaplastic astrocytomas and glioblastomas, the MDM2 gene being
frequently coamplified (6).
35 cycles of amplificationwere performed at 94°Cfor 1 min, 60°Cfor 1 mm,
and 72°Cfor 1 min with (CDKN2/MTSJ and MTS2) or without (1063.7 and
reverse,
AATGC(TFGGCATAAGGGAC).
Thirty
to
cl.b) 5% DMSO. The PCR products were separated on a 1.2% low-melting
point agarose gel. The bands were excised and the PCR products were purified
by Magic PCR kit (Promega,
as described
identical.
Madison,
WI) and used as probes. All primers are
by Kamb et a!. (7), who showed
These
probes
were initially
MTSJ(CDKN2)
hybridized
several cell lines including T98G, U118MG,
to TaqI-digested
and p16 to be
DNA from
and normal human leukocyte
DNA. Because of the high homology of exon 2 in CDKN2 and MTS2,both the
CDKN2 (exon 2) probe and the MTS2 probe identified identical band pairs in
normal DNA, 3.3 and 1.3 kilobases, respectively
(data not shown). In T98G
DNA, only the 1.3-kilobase band was detected while neither band was found
in U118MG DNA. T98G has a homozygous deletion only at the CDKN2locus
while U118MG has a much larger deletion including both the CDKN2 and
MTS2 loci. Accordingly, the 3.3-kilobase band corresponds to CDKN2 exon 2
and the 1.3-kilobase band to MTS2,and the CDKN2 exon 2 probe was used to
analyze both loci. The CDKN2 exon 1 probe gave a single 1.0-kilobase band
(datanotshown).
Received 9/26/94; accepted 11/3/94.
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.
1 This work was supported by grants from the Swedish Cancer Society and the Funds
of the Karolinska Institute.
2 These authors contributed equally to this work.
3 To whom requests for reprints should be addressed, at Institute for Oncology and
Pathology, Division of Tumor Pathology, Box 100, Karolinska Hospital, 5-171 76
Stockholm, Sweden.
A probefor the cyclin Dl gene was generatedby reversetranscription-PCR
using the primers TCCTGTGCTGCGAAGTGGAAAC
GGGGCfCCFCAGGUC
and cDNA
from
the A431
and AAGTFGTF
cell line. A 655-base
pair PCR fragment corresponding to bases 158 to 812 of the cyclin Dl cDNA
sequence (EMBL Accession No. M64349) was subcboned into the pCRII
vector using the TA-cloning kit (Invitrogen, San Diego, CA), and purified
plasmid was used as a probe. The identity of the probe for cyclin Dl was
confirmed by sequencing using the Sequenase Version 2.0 DNA Sequencing
6321
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CDKN2 DELE11ONS AND CDK4 AMPLWICATIONS
Kit (USB) (data not shown). The DNA probes for CDK4 and MDM2 have been
described
previously
Densitometric
Analysis.
Densitometric
and calculated
as described
signals
were
using
measured
formula
GB23
GB14
GB29
AA49
AA18
(6).
formed
measured
interest― (LOl)
GB22
IN GUOMAS
hybridization
analysis of allele dosage was per
previously
the ImageQuant
signals
were
at the control locus D2S44
(4).
Briefly,
software,
normalized
B
hybridization
and the “locusof
against
T
B
T
1063.7
the signals
(CL) on the same blot according
to the
1.8
No. of alleles =
2 X N X LOIm
B
T
B
T
=@
B
T
B
T
0.2
1.1
1.4
0.2
0.1
CDKN2
LOI(B)
with
@
CL(B@l) CL(B@2)
— CL(T@l
0.6
1.0
0.2
0.6
1.2
1.2
2.0
0.2
0.2
1.8
1.0
MTS2
CL(T@2)
2
where T represents
tumor, B blood, and A 1 and A2 larger and smaller alleles,
ci .b
respectively.
For DNA extraction, tumor pieces containing a minimum of 70% tumor
cells were used. On the basis of this principle,
0 to 0.6 as representing
a homozygous
we consider
deletion,
an allele value of
0.9 to 1.3 as representing
a
1.2
hemizygous deletion, and values of 1.7 or more as representing retention of
both alleles.
significant
Only
an allele
copy
number
of 5 or more
was
1.6
considered
amplification.
Results
In a previous study we found a common region of homozygous
deletion in glioblastomas flanked by the D9S171 and JFNcrJw loci.
Nine homozygous deletions involving one or the other or both of these
loci were determined among the 47 glioblastomas studied (19%) (4).
The incidence of homozygous deletions in this region more than
doubled (41%) among the glioblastomas when 4 loci between the
Fig. 1. I@oci [cI.b (centromcric), M1@2, CDKN2, 1%3.7 (telomeric)J studied by
Southern blot analysis are shown for 4 glioblastoma cases (GB22, GB23, GB14, and
GB29) and 2 anaplastic astrocytomas (AA49 and AA18). B, constitutional WBC DNA T,
D9S171andtheIFNcvJw
lociwereexamined.
Nohomozygous
dele
tumor DNA. To assess loading of DNA, control hybridizations of the same Southern blots
tions had been identified previously among the anaplastic astrocyto
mas, yet one case which had previously shown loss of one allele at the
IFNa/w locus and 2 cases in which no losses had been identified at
either locus were found to have homozygous deletions located be
tween but not involving the D9S171 or the IFNcrJw loci.
The homozygous deletions in the glioblastomas are frequently
large. The smallest region in a single case is found in GB22 and
includes the MTS2 and CDKN2 loci (the status of the 1063. 7 locus
could not be determined in this case) with breakpoints between the
tumor DNA is given below the tumor lane (for estimation of allele values see “Materials
and Methods―).
GB22 showed the smallest region of homozygous deletion. The tissue
cl.b and MTS2 loci centromerically
and the CDKN2
and lFNctho
loci
telomerically (Figs. 1 and 2). The homozygous deletions in the ana
plastic astrocytomas (AA12, 49, and 18; Fig. 2) all involve a more
limited area with AA49 and AA18 (Figs. 1 and 2) limiting the loss of
both alleles to the CDKN2 and MTS2 loci with breakpoints centro
merically between MTS2 and cl.b and telomerically between CDKN2
and 1063. 7. A similar tebomeric breakpoint can be found in case GB23
(Figs. 1 and 2) which shows loss of one allele at the CDKN2 locus
with retention of both alleles at the 1063. 7 locus.
Case GB14 (Figs. 1 and 2) shows a complex pattern ofloss with the
retention of one allele at the MTS2 locus and loss of both alleles at all
surrounding loci suggesting that the MTS2 locus may not always be
included in the common region of loss. This is further supported by
the deletion mapping of the glioblastomas with losses of one allele.
Cases GB25 and GB29 retain both alleles at the MTS2 locus and lose
one at the CDKN2 locus and thus have centromeric breakpoints
between these loci. Of the loci studied, the common region lost thus
always includes only the CDKN2 locus.
When the incidence of losses (of one or both alleles) at all loci are
considered, alleles in the region between D9S171 and the lFNcrJo loci
were lost in 32 of 46 glioblastomas (70%) with CDKN2 and adjacent
at the highly informative D2S44 locus are shown. The allele value at each locus for the
sample used was determined histologically to contain approximately 80% tumor cells.
Note the loss of one allele at cl.b, loss of both alleles at MTS2 and CDKN2.The 1063.7
locus was not determinable but both alleles were retained at the iFNaJw locus (see Fig.
2). GB23 shows boss of one allele at the MTS2 and CDKN2 loci with the centromeric
breakpoint between D9S126 (see Fig. 2) and MTS2 but with the tebomeric breakpoint
between CDKN2 and 1063.7. GB14 retains one allele at the MTS2 locus despite losing
both alleles at the surrounding loci, placing the MTS2 gene outside the region of common
loss. GB29 shows retention of all centromeric alleles including the hflT2 gene and then
shows loss of one allele at the CDKN2locus. Both alleles were determined to be retained
at the iFNcsJw locus. AA49 and AA18 show retention of at beastone allele at the flanking
loci cl.b and 1063.7 with loss of both alleles at the intervening MTS2 and CDKN2 lad.
loci (MTS2 and 1063. 7) showing the highest incidence of loss. The
anaplastic astrocytomas showed loss of genetic material from the
same region in 10 of 16 cases (63%) but the highest incidence did not
occur at the CDKN2 and adjacent loci (5 of 16). The genetic loss was
more common at the D9S126 and IFNoJco loci, often with loss of one
allele at both these loci, with retention ofboth alleles at all intervening
loci (Fig. 2).
When all tumors were studied for amplification of the CDK4 and
MDM2 genes, CDK4 was found to be amplified in 20% of the
glioblastomas and 19% of the anaplastic astrocytomas. MDM2 was
coamplified in five of the glioblastomas and in two of the anaplastic
astrocytomas (Fig. 2). Amplification occurred preferentially among
the glioblastomas and the anaplastic astrocytomas which retain both
alleles at all loci in the immediate region of the CDKN2 locus. Two
glioblastomas, GB28 and GB7, show amplification of CDK4 and
MDM2 in the presence of losses of alleles at the CDKN2 and sur
rounding loci (Fig. 2). GB28 has a homozygous deletion which
stretches centromerically from between the D9S126 and the cl.b loci,
6322
Downloaded from cancerres.aacrjournals.org on June 15, 2017. © 1994 American Association for Cancer Research.
@
‘@
e
CDKN2 DELEtiONS
A
cen
CD
@
@
@
@
@
tel
‘-
c*1
@; .@Cl) @2
@
@
@
@
@
9p
C@1
N.
r'@
AND CDK4 AMPLIFICATIONS
to a position telomerically between the 1063. 7 and the IFNcsJw loci.
GB28 shows an allele copy number ofjust over 5 for the CDK4 gene.
GB7, which shows loss of one allele at all loci between the cl.b and
@B
:@
c@
the 1063.7 loci has a high level of CDK4 and MDM2 amplification
GB97
GB2I
GB69
GBI4
— — —
— — —
— —
—
—
GB32
GB2S
GBI7
— — —
— — — —
— — — —
:
GBI6
GB45
— — —
——n—
:
:LIIII LIII
GBI5O
GBI5I
GB2
GBIOI LIII
GB4O
GB4
GBI
(Fig. 2). None of the three anaplastic astrocytomas with losses in the
region of the CDKN2 gene showed evidence of amplification of
CDK4 or MDM2.
All of the low-grade astrocytomas were assessable at the CDKN2,
MTS2, CDK4, and MDM2 loci and no evidence of any losses of alleles
or amplification of genes was found. All 70 tumors were additionally
screened for amplification of the cyclin Dl gene. However, no am
plification was found in this series.
— — !
LIII
—
:
—
!
LIII
—
: LIII LIII
— — — —
— — — —
— — — —
— —
— — —
— — — —
— :
LIII
— LIII LIII
— : 11111
L@J
— :
— LIII LIII
:
LII
LIII
Discussion
LIII
The results of this study implicate the CDKN2 gene to be involved
in the development of anaplastic astrocytomas and glioblastomas.
Homozygous deletion of the region encompassing the CDKN2 gene
was found in a high percentage of glioblastomas (41%). In addition,
we found the same region homozygously lost in 19% of the anaplastic
m
:
—
GB38
@
@
GB6
LIII
GB22
—
GB7
@
GB8
GB5
E@I ___
__
@LI __
ELI
@
GB23
GB39
@
GB29 E@
___
L@@II
LIII
@
GB9O
@
GB142
GBI3 E@
@
@
@
@
___
___
__
___
___
:: ___
_____
:
:
LII
LIII
LII LII
LIIIEli
___
__
LII
:
:
:L@I L@J
LIII: @II
L@II
:
:@:@
:L@IIL@II
LII :L@IILIII
GBI2
GB15
GB27
GB44
AAI2
El
E@I
E1
:
E@I LII
LIII LII
LII EIIILIIILII
LII
LII LII LIII
—
@J
:LLI LIII
:LII LIII
:
LII
LII LII LII EII1
————
AA49
AAI8
LIII
:
—
AA2
AA13
ELIILII EEl LIII
AA5O
AA34
ELI
LIII LIII LIII
LII
:
:
@
LIII LIII L@
LIII LIII LII
@
@
AA45
AAI7
IIIII
LIII
LIII
LIIILII
:
: .
AA52
AA3
AA2O
A
LIII
E@
LLI
LII
of one allele in the same region. Another area telomeric to the 1063.7
locus and including
EIIII LIII
Homozygousdeletion
<5
.@...: s.is
locus is frequently
involved
in inter
occurs more frequently in cell lines than in tumors (16, 17), the
band
Retention
olboth
alleles
16.3O@@
the IFNaJw
stitial deletions in GB1O, AA14, AASO, AA34, and AA19. These two
interstitial deletions are commonly found in the same tumor.
In the light of reports that suggest that mutation of the CDKN2 gene
Hemlzygousdeletion
am Retention
ofatleast
one
allele
B
addition GB1O,AA14, AA5O,AA34, and AA4 show interstitial bosses
LIIII LIII
LIIIII LIII
Partial homozygous and hemizygous deletion with aberrant
@
study (4) inasmuch as they are restricted to a region located inbetween
the loci examined formerly.
The distance between the CDKN2 gene and its flanking loci, MTS2
and 1063. 7 has been estimated to be between 20 and 30 kilobases (7).
In this study, breakpoints have been demonstrated within this rela
tively short distance in a number of the tumors. Breakpoints occurred
between the MTS2 locus and the CDKN2 locus in GB25, GB29, and
GB14, and between CDKN2 and 1063. 7 in GB23, AA18, and AA49.
The common region of loss, when data from both the homozygous
deletions and losses of one allele are combined, is thus between the
MTS2 locus centromerically and the 1063. 7 locus telomerically and
encompasses a region, estimated to be 40—50kilobases, within which
the CDKN2 gene lies.
The finding that amplification of the CDK4 gene occurs in up to
50% of the glioblastomas which show no abnormalities in the region
of the CDKN2 gene suggests that aberrations of the cell cycle control
mechanism are critical for the development of this tumor form.
Aberrations of this mechanism are not involved in the development of
astrocytomas. They first appear among anaplastic astrocytomas and
are most frequent among glioblastomas and thus may be involved in
the progression of these tumors. When aberrations of these two genes,
the proteins of which are involved in the control of the phosphoryl
ation of Rbl are included, 85% of the glioblastomas in the series show
abnormalities. Cyclin Dl, which is also part of this cell cycle-regu
latory mechanism, was not found to be amplified in this series. Thus,
amplification of cyclin Dl does not appear to be a factor involved in
the progression of these tumors.
Some of the findings suggest that CDKN2 may not be the only
tumor suppressor gene of interest on 9p. The interstitial homozygous
deletion in GB7 encompasses areas centromeric to the cl.b locus. In
:@I LII : @j
:LIIILIII
AA4
AA16
@
astrocytomas. The latter deletions could not be detected in a previous
:LII LII
:
:
LIII
LII ELIJ
LII E@I LII LLI
GB1O5 LIII
AAI9
@
LII
•
IIJE::RRRRE:J@R
AAI4
@
:
LII
GBIOO
@
:
LIII
GB25
GBIO
GB26
GB37
___
@::i
LIII ___
GB144
GB36
GB34 LIII
@
@
—
GB3O
GB24
GB4I
IN GLIOMAS
present data document that the region containing the CDKN2 gene is
>30
Fig. 2. A, summary of the status of alleles at all loci studied between D9S126 and
IFNaJw in all glioblastomas and anaplastic astrocytomas of the series. The results at the
CDKN2 locus represent a combination of the findings using both the CDKN2 exon 1 and
exon 2 probes, which gave similar allele values. Loci for which no data are given are loci
at which the case was not informative or where quantitative analysis gave intermediate
values, not permitting a determination of the state of the alleles. B, summary of the status
of amplification at the CDK4 and MDM2 loci. Copy numbers are indicated.
6323
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CDKN2 DELETIONS AND CDK4 AMPLIFICATIONS
definitely involved in the majority of glioblastomas and some ana
plastic astrocytomas. It remains to be seen whether there are any other
genes in this limited, commonly deleted region. Recently, MTS2 has
been shown to code for another inhibitor of CDK4 and CDK6 (15).
Although MTS2 is not included in our commonly deleted region, loss
of this gene could also contribute to tumorigenesis, because MTS2 was
found to be deleted in addition to CDKN2 in a high percentage of
cases studied. Mutational analysis of the CDKN2 gene in the cases
retaining one or both alleles is ongoing. Such studies and the effects
of the expression of the wild type gene on the phenotype of tumor
cells will confirm or exclude the CDKN2 gene as a tumor suppressor
gene involved in the progression of gliomas.
IN GUOMAS
malignant gliomas: preliminary mapping of the amplicons shows preferential involve
ment of CDK4, SAS, and MDM2. Cancer Res., 54: 4299—4303, 1994.
7. Kamb, A., Gruis, N. A., Weaver-Feldhaus,J., Liu, 0., Harshman, K., Tavtigian, S. V.,
Stockert, E., Day, R. S., III,, Johnson, B. E., and Skolnick, M. H. A cell cycle
regulator potentially involved in genesis of many tumor types. Science (Washington
DC),264:436—440,
1994.
8. Nobori, T., Miura, K., Wu, D. J., Lois, A., Takabayashi, K., and Carson, D. A.
Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers.
Nature (Land.), 368: 753—756,
1994.
9. Serrano, M., Hannon, G. J., and Beach, D. A new regulatory motif in cell cycle
control causing specific inhibition of cycbin/CDK4. Nature (Lond.), 366: 704—707,
1993.
10. Kamb, A., Shattuck-Eidens, D., Eeles, R., Liu, 0., Gruis, N. A., Ding, W., Hussey,
C., Tran,T., Mild,Y., Weaver-Febdhaus,
J., McClure,M.,Aitken,J. F., Anderson,
D. E., Bergman, W., Frants, R., Gobdgar, D. E., Green, A., MacLennan, R., Martin,
N. G., Meyer, L. J., Youl, P., Zone, J. J., Skolnick, M. H., and Cannon-Albright, L. A.
Analysis of the pitS gene (CDKN2) as a candidate for the chromosome 9p melanoma
susceptibility locus. Nat. Genet., 8: 22—26,1994.
11. Hussussian, C. J., Struewing, J. P., Goldstein, A. M., Higgins, P. A. T., Ally, D. S.,
Acknowledgments
Sheahan, M. D., Clark, W. H., Jr., Tucker, M. A., and Dracopoli, N. C. Germline p16
mutations in familial melanoma. Nat. Genet., 8: 15—21,1994.
We thank Dr. Karin Messerle for critical reviewing of the manuscript.
12. Mori, T., Miura, K., Takahisa, A., Nishihira, T., Mon. S., and Nakamura, Y. Frequent
somatic mutation of the MTSJ/CDK41 (multiple tumor suppreamr/cyclin-dependent
kinase 4 inhibitor) gene in esophageal squamous cell carcinoma. Cancer Rca., 54:
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CDKN2 (p16/MTS1) Gene Deletion or CDK4 Amplification
Occurs in the Majority of Glioblastomas
Esther E. Schmidt, Koichi Ichimura, Guido Reifenberger, et al.
Cancer Res 1994;54:6321-6324.
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