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Journal of Virology, March 2000, p. 2161-2168, Vol. 74, No. 5
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Sint1, a Common Integration Site in
SL3-3-Induced T-Cell Lymphomas, Harbors a Putative Proto-Oncogene with
Homology to the Septin Gene Family
Annette Balle
Sørensen,1
Anders H.
Lund,1,
Steen
Ethelberg,1,
Neal G.
Copeland,2
Nancy A.
Jenkins,2 and
Finn
Skou
Pedersen1,3,*
Department of Molecular and Structural
Biology1 and Department of Medical
Microbiology and Immunology,3 University of
Aarhus, DK-8000 Aarhus C, Denmark, and Mammalian Genetics
Laboratory, ABL-Basic Research Program, NCI-Frederick Cancer Research
and Development Center, Frederick, Maryland
217022
Received 26 August 1999/Accepted 7 December 1999
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ABSTRACT |
The murine retrovirus SL3-3 is a potent inducer of T-cell lymphomas
when inoculated into susceptible newborn mice. Previously, DNAs from
twenty SL3-3-induced tumors were screened by PCR for provirus
integration sites. Two out of 20 tumors demonstrated clonal provirus
insertion into a common region. This region has now been isolated and
characterized. The region, named SL3-3 integration site 1 (Sint1), maps to the distal end of mouse chromosome 11, corresponding to human chromosome 17q25, and may be identical to a
mouse mammary tumor virus integration site in a T-cell lymphoma, Pad3. Two overlapping genomic
clones spanning about 35 kb were isolated and used as a starting point for a search for genes in the neighborhood of the virus integration sites. A genomic fragment was
used as a hybridization probe to isolate a 3-kb cDNA clone, the
expression of which was upregulated in one of two tumors harboring a
provirus in Sint1. The cDNA clone is predicted to encode a
protein which shows 97.0% identity to a human septin-like protein
encoded by a gene which has been found as a fusion partner gene of MLL in an acute myeloid leukemia with a t(11;17)(q23;q25). Together these
findings raise the possibility that a proto-oncogene belonging to the
septin family, and located about 15 kb upstream of the provirus
integration sites, is involved in murine leukemia virus-induced T-cell lymphomagenesis.
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INTRODUCTION |
The induction of lymphomas and
leukemias by the non-oncogene-bearing murine leukemia viruses (MLVs) is
a complex process, comprising many steps of which the most well-defined
one involves long terminal repeat (LTR) deregulation or impairment of
cellular proto-oncogenes or tumor suppressor genes (29, 38).
Proviral tagging of critical loci has during the last 15 years proved
to be a powerful tool to identify genes associated with specific diseases. For example, c-myb, Evi1, and
Evi2 are genes/common integration sites which mainly are
correlated with MLV-induced myeloid leukemias (4, 23, 33,
39), while c-myc, Pim1, Mlvi1/pvt1, Evi3, and Evi5 primarily
are associated with MLV-induced lymphomas (8, 13, 18, 21, 31,
37). Although there is no doubt that insertional mutagenesis
plays a major role in tumor development, insertion into a common
integration site for a specific tumor type has never been reported to
be 100%, revealing the complexity of the process. Some proto-oncogenes
(or common integration sites) may function redundantly as well as
cooperate with other proto-oncogenes (17).
In addition to depending on the type of disease induced, the specific
genes that will be tagged by a provirus depend on virus type. This is
illustrated by the difference between SL3-3 MLV and Moloney MLV
(Mo-MLV). Despite the fact that both viruses induce T-cell
lymphomas with similar latency periods, the frequencies of
integrations into specific sites are different. For example, while
Mo-MLV and SL3-3 both exhibit insertions in the c-myc gene in 20 to 40% of the induced end-stage tumors, the frequencies of
insertions observed in the Pim1 locus amount to 15 to 65%
of the Mo-MLV-induced tumors but less than 1% of the SL3-3-induced tumors (1, 8, 9, 15, 24, 29, 31, 35, 36). It thus appears
that even viruses of similar disease specificities may exploit
different gene activation pathways.
Previously, we have by a PCR-based method isolated and determined the
sequences of provirus integration sites in twenty tumors induced by
SL3-3 MLV (34, 35). We found that in two independent tumors
a provirus had inserted into the same region. In essence, retroviral
integration is random; thus the finding of two independent insertions
into a common site strongly indicates that a linked host gene plays a
role in the tumorigenic process.
We report here on further analysis of the integration site region as
well as on the isolation of a cDNA clone representing a gene in this
region. The chromosomal mapping of the region, which was named SL3-3
integration site 1 (Sint1), to the distal end of mouse
chromosome 11 suggests that Sint1 overlaps or is identical
to the Pad3 locus previously identified as an integration site in an mouse mammary tumor virus (MMTV)-induced T-cell lymphoma (28). Taken together with the finding that the associated
Sint1 cDNA seems to encode a protein homologous to a human
septin-like protein that has been found as a fusion partner of MLL in
an acute myeloid leukemia, this indicates that Sint1 cDNA
may identify a novel proto-oncogene involved in mouse T-cell lymphomagenesis.
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MATERIALS AND METHODS |
Genomic DNA and RNA analyses.
DNA was extracted from frozen
tumor tissues as previously described (14). Tumors
originated from experiments described by Hallberg et al.
(14). Total RNA was isolated from frozen tumor tissues or
cell lines by RNA Isolator (Genosys Biotechnologies, Inc.) following
the manufacturer's recommendations.
For Northern analysis 25 µg of total RNA was separated on a 1.2%
agarose-formaldehyde gel, transferred to nylon membranes (Zeta-Probe;
Bio-Rad) by alkaline (50 mM NaOH) blotting, and hybridized in 0.5 M
Na2HPO4 (pH 7.2)-7% sodium dodecyl sulfate
buffer with 32P-labeled (randomly primed DNA labeling) DNA
probes. The multiple-tissue Northern and the mouse embryo Northern
filters that were purchased from Clontech Laboratories, Inc., contain
approximately 2 µg of poly(A)+ RNA per lane.
Hybridization procedures were as recommended by the manufacturer. The
following probes were used: probe A, a genomic preintegration PCR probe
(35); probe B, a genomic 900-bp PstI fragment;
probe C, a 700-bp EcoRI cDNA fragment; human
-actin, an
internal control probe.
RNase protection assay.
The assays were performed with the
RPA III (RNase protection assay) kit from Ambion Inc. In essence, the
supplied instruction manual was followed; 5 µg of tumor RNA and
105 cpm of RNA probe were used. The gel-purified
radiolabeled RNA probes were made by in vitro transcription from T7
promoters according to standard protocols. The Sint1 probe
and the control mouse
-actin probe were transcribed from gel
purified-PCR products using the following primers: Sint1
probes 5'-GCA GTA AGC TTC CCC GAA TTC AAG GGA TCC ATT TAG
GTG ACA CTA TAG AAC CCT GGC TGA CAA CCC TAG AGA
TGC CAT-3' (SP6) and 5'-TAC AGA AGC TTT ACA GAA TTC CAG
GGA TCC TAA TAC GAC TCA CTA TAG GCG TAA
CTG TCA GCT TCA TTC GAA CCC CCT-3' (T7); mouse
-actin
probes 5'-GCA GTA AGC TTC CCC GAA TTC AAG GGA TCC ATT TAG
GTG ACA CTA TAG AAC CCG CCC TAG GCA CCA GGG TGT
GAT GGT-3' (SP6) and 5'-TAC AGA AGC TTT ACA GAA TTC CAG
GGA TCC TAA TAC GAC TCA CTA TAG GCG TAT
CGG TGA GCA GCA CAG GGT GCT CCT-3' (T7). The underlined
parts of the primers correspond to SP6 or T7 promoters, with the
boldface letter denoting the transcriptional start site, while the
italicized parts correspond to the hybridizing sequences of the
primers. The expected sizes of the unprotected and RNase-protected RNA probes are as follows: Sint1 probes, 378 and 325 bp,
respectively; mouse
-actin probes, 263 and 210 bp, respectively.
RNase-resistant products were analyzed by electrophoresis and
autoradiography, and quantification of radioactive fragments was
performed on the PhosphorImager SF (Molecular Dynamics, Inc.). Primers
were from DNA Technology A/S, Aarhus, Denmark.
RT-PCRs.
Reverse transcription-PCRs (RT-PCRs) were carried
out using primer 10 (see below) for the first-strand cDNA synthesis
(first-strand cDNA synthesis kit; Amersham Pharmacia Biotech) on
approximately 2 to 4 µg of total RNA from tumors or spleen. PCR
amplifications of the cDNAs were performed in two rounds. In the
initial PCRs of eight cycles (first PCR; Fig.
1), 5 µl out of 15 µl of first-strand cDNA synthesis mixture was used as the template and the following primer sets were employed: 1 plus 2, 3 plus 4, and 5 plus 6 (Fig. 1).
In the nested PCR (second PCR; Fig. 1) of 35 cycles, 2 µl out of 50 µl of the first PCR mixture was used as the template and the
appropriate primer sets (1 plus 2, 1 plus 7, 3 plus 9, 5 plus 6, and 8 plus 6) were employed. For analysis, 10 µl out of 50 µl from the
second PCR mixture was electrophoresed on an ethidium bromide-stained
2% agarose gel. The sequences of the primers were as follows: primer
1, 5'-TTGCAGCCAGCAGAGCCCACTTAAACT-3'; primer 2, 5'-TTCCTCCTGCAGGTACTTCTCATAT-3'; primer 3, 5'-CAGCGGATCACTGCAGACCTGCTGT-3'; primer 4, 5'-GGGCAGGCAGCTGAGGGCGCTGT-3'; primer 5, 5'-GCTAGCTTTCTGCAGCCCAGAAGT-3'; primer 6 (nested primer 10),
5'-GGGTCTAGAGCTCGAGTCACT-3'; primer 7, 5'-CTGCGCATCTGCTCCAGGATGGAGT-3'; primer 8, 5'-CTGTTCGTCTCACCAGGCCGGTCCACGT-3'; primer 9, 5'-TGGGAAGAGATGGATGGAGGCAGGT-3'; primer 10 (poly[T] primer), 5'-GGGTCTAGAGCTCGAGTCACTTTTTTTTTTTTTTTTV-3' (V = A, G, or C). All primers were purchased from DNA Technology A/S).

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FIG. 1.
Primer positions for RT-PCR analyses. The 3.0-kb
Sint1 cDNA is indicated as a line with the identified exon
included as a shaded box. Arrows indicate positions and numbers of
primers. The expected (brackets) and observed sizes of the PCR
fragments are indicated. The PCR analyses were performed in two rounds
(see Materials and Methods), and the products from the second PCR were
analyzed by gel electrophoresis (not shown).
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Library screening.
The genomic library was made of partially
MboI-digested mouse genomic (ES SV129 Dg) DNA inserted into
BamHI-digested
GEM12 vectors. Hybridizations with the
preintegration PCR probe A and subsequent purifications of positive
clones were done by standard techniques (30). Two positive
clones were obtained. The cDNA library was a mouse embryonic cDNA
library in a
ZAP/EcoRI vector (Stratagene). Screening with probe B
and in vivo excision (according to a protocol from manufacturer)
resulted in one positive clone.
Sequence analysis.
Sequencing reactions were performed with
a Thermo Sequenase II dye terminator cycle sequencing kit (Amersham
Pharmacia Biotech), and reaction products were analyzed on an automated
DNA sequencer (373A DNA sequencer; Applied Biosystems Inc.). Nucleotide
sequences were compared with sequences in the GenBank, EMBL, and EST
databases by using Wisconsin package EGCG [version 8.1.0(a)] FASTA
and BESTFIT programs.
Interspecific mouse backcross mapping.
Interspecific
backcross progeny were generated by mating (C57BL/6J × Mus
spretus) F1 females and C57BL/6J males as described previously (6). A total of 205 N2 mice were used
to map the Sint1 locus (see below for details). DNA
isolation, restriction enzyme digestion, agarose gel electrophoresis,
Southern blot transfer, and hybridization were performed essentially as
described previously (16). All blots were prepared with
Hybond-N+ nylon membrane (Amersham). The probe, a 392-bp
fragment of mouse genomic DNA (probe A; Fig. 2) was labeled with
[
-32P] dCTP using a randomly primed labeling kit
(Stratagene); washing was done to a final stringency of 0.5× SSCP
(0.06 M NaCl, 7.5 mM sodium citrate, 10 mM sodium phosphate)-0.1%
sodium dodecyl sulfate at 65°C. A fragment of 4.7 kb was detected in
SphI-digested C57BL/6J DNA, and a fragment of 3.8 kb was
detected in SphI-digested M. spretus DNA. The
presence or absence of the 3.8-kb SphI M. spretus-specific fragment in backcross mice was monitored.
A description of the probes and restriction fragment length
polymorphisms (RFLPs) for the loci linked to
Sint1,
including
Grin2c,
Hfh4, and
P4hb, has
been reported previously (
12). Recombination
distances were
calculated using Map Manager, version 2.6.5. Gene
order was determined
by minimizing the number of recombination
events required to explain
the allele distribution
patterns.
Nucleotide sequence accession numbers.
The nucleotide
sequences of the Sint1 cDNA (Fig. 6) and the genomic
subclone shown in Fig. 5 have been assigned EMBL data bank accession
no. AJ250723 and AJ250724, respectively.
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RESULTS |
Two proviruses inserted into a common region.
Previously, in
order to identify proto-oncogenes involved in SL3-3 MLV-induced T-cell
lymphomagenesis, we have amplified by PCR and analyzed provirus
integration sites in tumor DNAs (34, 35). In brief, from one
such integration site of which the flanking sequence showed no homology
to any known sequences in available databases, a unique PCR probe of
392 bp was generated (probe A; Fig. 2A).
This probe was hybridized to Southern blots containing HindIII-digested DNA from 20 SL3-3-induced lymphomas,
and thus the clonality of the original integration was verified.
Moreover, the hybridization revealed a rearranged fragment in the same
region of DNA in an independent tumor (35). That this
rearrangement was also due to an integrated provirus was confirmed by
combinatorial PCRs using provirus-specific primers a and b together
with primers 1 and 2 (primer localizations are indicated in Fig. 2A). A
PCR fragment of about 3.0 kb was amplified by primer 2 and primer a.
Taken together, these results demonstrated that a provirus had
integrated into a common DNA region in two independent tumors, with the
integration sites being separated by approximately 2.5 kb and the
orientations of the integrated proviruses being opposite relative to
each other (Fig. 2A). The DNA region was named SL3-3 integration site 1 (Sint1).

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FIG. 2.
(A) Relative locations and orientations of the
integrated proviruses in two independent tumors (15 and 16). Box,
preintegration site PCR probe A; arrows 1 and 2, primers used to
amplify probe A; arrows a and b, provirus-specific primers;
H, HindIII restriction site. (B) Restriction
map of the cloned Sint1 locus. Upper lines indicate the two
overlapping genomic -phage clones, while the bottom line shows the
resulting map. SacI (S), XhoI (X),
PstI (P), HindIII (H), and EcoRI
(E) sites are indicated. Underlined are the CpG indicator enzymes (see
text). Dotted lines, regions only partly analyzed by restriction enzyme
mapping and sequencing; boxes A and B, hybridization probes; triangles,
provirus integration sites.
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To obtain clones that covered the
Sint1 region, a genomic

-phage library was screened with probe A. Two overlapping clones
covering about 35 kb were obtained, and a physical map of
Sint1 was constructed (Fig.
2B).
Chromosomal mapping of Sint1.
The integration site
sequences did not reveal any open reading frames (ORFs), and the
integration site probe (probe A; Fig. 2) did not hybridize to RNA from
a murine T-cell line (data not shown), suggesting that the proviruses
might have inserted outside an expressed region. Accordingly, the
Sint1 region could contain already-known proto-oncogenes. In
order to test this, the chromosomal location of Sint1 was
determined by interspecific backcross analysis using progeny derived
from matings of ([C57BL/6J × M. spretus]F1 × C57BL/6J) mice. This interspecific
backcross mapping panel has been typed for over 2,900 loci that are
well distributed among all the autosomes as well as the X chromosome
(6). C57BL/6J and M. spretus DNAs were digested
with several enzymes and analyzed by Southern blot hybridization for
informative RFLPs using probe A (Fig. 2). The 3.8-kb SphI
M. spretus RFLP (see Materials and Methods) was used to
monitor the segregation of the Sint1 locus in backcross
mice. The mapping results indicated that Sint1 is located in
the distal region of mouse chromosome 11 linked to Grin2c,
Hfh4, and P4hh. Although 108 mice were analyzed
for every marker and are shown in the segregation analysis (Fig.
3), up to 147 mice were typed for some
pairs of markers. Each locus was analyzed in pairwise combinations for
recombination frequencies using the additional data. The ratios of the
total number of mice exhibiting recombinant chromosomes to the total
number of mice analyzed for each pair of loci and the most likely gene
order are as follows: centromere-Grin2c-(2 of
147)-Sint1-(0 of 128)-Hfh4-(3 of
136)-P4hb. The recombination frequencies (expressed as
genetic distances in centimorgans [cM] ± the standard error) were as
follows: centromere-Grin2c-(1.4 ± 1.0, cM)-(Sint1, Hfh4)-(2.2 ± 1.3 cM)-P4hb. No recombinants were detected between
Sint1 and Hfh4 in 128 animals typed in common,
suggesting that the two loci are within 2.3 cM of each other (upper
95% confidence limit). This same region is known to include another
retroviral integration site, Pad3, identified as an MMTV
integration site in DNA from a T-cell tumor (28).

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FIG. 3.
Sint1 maps in the distal region of mouse
chromosome 11. Sint1 was placed on mouse chromosome 11 by
interspecific backcross analysis. The segregation patterns of
Sint1 and flanking genes in 108 backcross animals that were
typed for all loci are shown at the top. For individual pairs of loci,
more than 108 animals were typed (see text). Each column represents the
chromosome identified in the backcross progeny that was inherited from
the (C57BL/6J × M. spretus)F1 parent.
Black, boxes, presence of a C57BL/6J allele; white boxes, presence of
an M. spretus allele. The number of offspring inheriting
each type of chromosome is listed at the bottom of each column. A
partial chromosome 11 linkage map showing the location of
Sint1 in relation to linked genes is shown at the bottom.
Recombination distances between loci in centimorgans are shown to the
left of the chromosome, and the positions of loci in human chromosomes,
where known, are shown to the right. References for the human map
positions of loci cited in this study can be obtained from the Genome
Data Base, a computerized database of human linkage information
maintained by the William H. Welch Medical Library of Johns Hopkins
University (Baltimore, Md.).
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The distal region of mouse chromosome 11 shares a region of homology
with human chromosome 17q25 (summarized in Fig.
3), suggesting
that the
human homolog of
Sint1 will map to 17q25 as
well.
Identification of a Sint1-linked cDNA.
To identify
possible genes localized in the Sint1 regions, the genomic
clones were digested with the rare-cutting enzymes SacII
(CCGC
GG), EagI (C
GGCCG), and BssHII
(G
CGCGC). A cluster of sites for these enzymes would indicate the
presence of CpG islands, which are associated with the promoter regions
of many genes (2, 20). The restriction endonuclease
digestions of the
clones revealed no such cluster. However, both
SacII and EagI cut once in the Sint1
region as indicated in Fig. 2B. Since the SacII cutting site
is located very close to the end of genomic
clone 1, it seemed
possible that this site was part of a cluster of
SacII/EagI/BssHII cutting sites, and
thus the 3.5-kb NotI/HindIII subclone of
clone 1 became the starting point for a search for Sint1
genes. From this subclone, a PstI fragment (probe B; Fig. 2B) was isolated and used as a probe in Northern blot analyses with
mRNA from different mouse tissues and from mouse embryos (Fig.
4). Although weakly expressed, a
predominant transcript of about 2.4 kb was seen in all examined tissues
except skeletal muscle. Probe B was then employed in an embryo cDNA
library screen by which one cDNA clone of about 3.0 kb was obtained.

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FIG. 4.
Northern blot analyses of Sint1 expression.
All three panels are identical Northern blots hybridized with the
probes indicated at the left. The blots contain about 2 µg of
poly(A)+ RNA per lane from eight different mouse tissues
(left) and from mouse embryos at different time points (right). Size
markers (in kilobases) are at the left of each autoradiogram.
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The sequences of the genomic 3.5-kb subclone as well as those of the
cDNA clone were determined, and it was found that an
exon of 132 bp
with conserved 5' and 3' splicing signals is located
in the genomic
PstI fragment (Fig.
5) and
that the sites of the
provirus integrations are located about 15 kb 5'
of this exon.
The integrity and the 3' end of the cDNA clone were
verified by
RT-PCRs employing primers located both inside and outside
the
identified exon as shown in Fig.
1, and the obtained PCR fragments
all showed the expected sizes (data not shown).

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FIG. 5.
Correlation between Sint1 genomic region and
Sint1 cDNA. (Top) Part of the genomic region; (middle)
genomic 3.5-kb HindIII/NotI subclone;
(bottom) corresponding cDNA clone. Triangles, provirus integration
sites. Restriction enzyme site abbreviations are as defined for Fig. 1.
Hybridization probes are shown as boxes A, B, and C. The grey box
containing an arrow indicates the location and orientation of the exon
in the genomic clone as well as in the cDNA clone. The 5' and 3'
splicing signal (ss) sequences are shown with the conserved intron
dinucleotides underlined.
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To address the apparent discrepancy between the transcript size
observed in the Northern blot analysis (~2.4 kb) and the size
of the
cDNA clone (~3.0 kb), a cDNA
EcoRI fragment of a 700-bp
(probe C; Fig.
5) was used as a probe on the same Northern blot
(Fig.
4). This time two major transcripts of about 3.0 and 4.0
kb were seen
in all examined tissues except skeletal muscle. However,
in some
tissues such as spleen and lung, the predominant transcript
was the
3.0-kb species, whereas in other tissues such as kidney
and testis,
only the 4.0-kb transcript seemed to be expressed.
The highest
expression was seen in liver, where both mRNA species
were found,
although the 4.0-kb transcript was expressed at much
higher levels. In
addition, some minor transcripts were seen,
e.g., a transcript of about
5.5 kb in brain and a transcript of
about 1.4 kb in testis. Likewise,
Northern blot analyses of RNA
from different lymphoid cell lines with
probe C showed different
transcript sizes with the 3.0- and 4.0-kb
transcripts as the predominant
ones (data not shown). Thus, it appears
that the overall RNA expression
pattern of this gene is
complex.
Sint1 encodes a septin-like protein.
The sequence
of the cDNA clone revealed a 5'-untranslated region (UTR) of at least
177 bp, an ORF of 1,002 bp, and a rather long 3'-UTR of 1,765 bp (Fig.
6). The 3'-UTR contains several copies of
the ATTT(A) motif, which is thought to confer instability to mRNAs
(10, 32), and a consensus poly(A) signal (AATAAA). The ORF is predicted to encode a polypeptide of 334 amino acid (aa) residues.

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FIG. 6.
Sint1 cDNA and predicted amino acid
sequences. In the 3'-UTR, the AT degradation motifs are underlined and
the polyadenylation site consensus sequence is boxed.
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A comparison of the predicted amino acid sequence encoded by the
Sint1 cDNA clone and sequences in the GenBank, EMBL,
Swissprot,
and EST databases showed a significant identity (97.0%) to
a human
brain cDNA-encoded protein and the human MSF (MLL septin-like
fusion) protein (
27) (Fig.
7).
The comparison analyses in addition
revealed significant homologies
(>70% identity) to proteins of
the septin family, a family of
proteins which were originally
identified by analysis of budding yeast
cell division cycle mutants
defective in cytokinesis (
5,
22)
and which were later isolated
from flies, mice, and humans (
19,
25,
26). The amino acid
sequences of these proteins contain
motifs that define the GTPase
superfamily (
3), although the
function of nucleotide hydrolysis
has not been determined. As indicated
in Fig.
7, the GTP-binding
motifs are also conserved in the
Sint1 cDNA-encoded protein.

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FIG. 7.
Comparison of the predicted amino acid sequences encoded
by Sint1 cDNA and a human brain cDNA (KIAA0991; accession
no., AB023208) or the human MSF cDNA (accession no., AF123052). The
KIAA0991 and MSF sequences are 100% identical in the region shown.
Boxed are the GTP-binding motifs. The sequences show 97.0% identity
and 97.9% similarity (it should be noted, however, that the KIAA0991
and MSF sequences are 88 and 234 aa residues longer, respectively, than
the Sint1 sequence). Alignment was performed with the
Genetics Computer Group program BESTFIT. Vertical lines, identical
residues; colons, well-conserved replacements that scored better than
0.5 in the PAM-250 matrix; dots, replacements scoring better than 0.1. The lengths of the Sint1, KIAA0991, and MSF sequences are
334, 422, and 568 aa, respectively.
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Sint1 cDNA expression in tumors with proviral
insertions at the Sint1 locus.
In order to examine if
provirus integrations at the Sint1 locus affected the
expression of the Sint1 cDNA, an RNase protection assay was
performed with RNAs from seven different SL3-3-induced tumors,
including the two tumors (tumor no. 15 and 16) that harbor a clonal
provirus insertion at the Sint1 locus (Fig. 2). The RNA probe employed spans 325 bp of the coding region of the
Sint1 cDNA (Fig. 8). When the
intensities of the protected Sint1 fragments were correlated
with the intensities of the protected internal control fragments (mouse
-actin), a clear upregulation (two- to threefold) of the
Sint1 cDNA expression in tumor 15 was observed (Fig. 8).
This indicates that a provirus integration at the Sint1 locus may have modified the expression of the linked Sint1
gene, the effect of which might have contributed to the development of
the tumor. On the other hand, no significant alteration of the
expression level of the Sint1 gene could be detected in
tumor 16, which may suggest a more complex mode of involvement of the Sint1 gene in tumor progression.

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FIG. 8.
RNase protection assay. (Top) RNase protection of RNA
from seven different SL3-3 MLV-induced tumors assayed with
Sint1 and mouse -actin RNA probes. Lane M, molecular DNA
size markers (200, 300, 400, and 500 bp). Arrows indicate the protected
fragments, the sizes of which are 325 bp for Sint1 and 210 bp for mouse -actin. (Bottom) Localization of the Sint1
RNA probe as well as the Sint1/ -actin values after
quantification of radioactive protected fragments in two experiments
(experiment 2 is the one shown at the top).
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DISCUSSION |
In order to identify genes involved in T-cell lymphomagenesis, we
have analyzed provirus integration sites in SL3-3-induced T-cell
tumors. We have identified a region of the mouse genome which has been
rearranged by a retrovirus insertion in 2 of 20 tumors. Hence, this
locus, which we have named Sint1, appears to define a region
that is important in the development of T-cell lymphomas. This is
further supported by the findings of Rajan and Dudley (28),
who identified an integration site, named Pad3, in an
MMTV-induced T-cell lymphoma. Pad3 cosegregates with the marker Hfh4 (HNF-3/forkhead homolog 4) as does
Sint1 (Fig. 3); hence Sint1 and Pad3
may constitute the same locus.
A genomic fragment was used as a probe to isolate a linked cDNA clone
of 3 kb. Enhanced levels of expression of this cDNA were detected in
one of the two tumors carrying a proviral insertion in the
Sint1 locus, strongly indicating that in this case
overexpression of the Sint1 gene, probably due to the
integrated provirus, did play a role in tumor initiation and/or
progression. Regarding the other tumor harboring a provirus in the
Sint1 locus, the picture is less clear, since no change of
expression was detected. As the normal expression pattern of the
Sint1 gene during differentiation is not known, there are
several possibilities concerning how and when the Sint1 gene
may be affected by the integrated provirus. For example, the
distinction between regulated and deregulated expression levels may at
certain stages be subtle, and a disturbance by an integrated provirus
may have profound effects on differentiation and/or growth but may not
necessarily have measurable effects on the expression level in the
end-stage tumor.
The distance of approximately 15 kb between the integrated proviruses
and the identified Sint1 exon and the fact that the two
proviruses have integrated in opposite directions relative to each
other indicate that the mechanism of activation is of the type referred
to as enhancer insertion (29, 38). In addition, preliminary
Northern blot analyses show no detectable differences in transcript
sizes in RNAs from tumors harboring proviruses inserted at the
Sint1 locus and from other tumors (data not shown). However, since the integrity of the Sint1 cDNA 5' end has not been
verified, the possibility still exists that the proviruses have
integrated in an intron of the Sint1 gene and thereby, at
least for tumor 16, which harbors a provirus inserted in the same
transcriptional orientation as that of the Sint1 gene, the
activation could have been 3'-LTR or 5'-LTR promotion in which a 5'
exon(s) might have been removed from the resulting transcript.
The putative Sint1 cDNA-encoded septin-like protein of 334 aa revealed a striking homology (97.0% identity; Fig. 7) to the encoded protein (568 aa) of MSF, a fusion partner gene of MLL in an
acute myeloid leukemia with a t(11;17)(q23;q25) (27), further strengthening the assumption that Sint1 is a
cancer-related gene. The same high degree of homology to a human brain
cDNA (KIAA0991)-encoded protein (466 aa) is seen. As mentioned, the
integrity of the 5' end of the Sint1 cDNA has not been
verified, and therefore we cannot exclude the possibility that the
full-length Sint1 cDNA might be several hundred base pairs
longer, which again might result in a longer ORF. In that case,
however, the extended region would show a homology of less than 50% to
the MSF (or KIAA0991) amino acid sequence. Despite this uncertainty,
Sint1 and MSF seem to represent the same gene in mice and
humans, respectively. First, the chromosomal locations match each
other. Sint1 maps to mouse chromosome 11 in an area of human
chromosome 17q25 homology (Fig. 3), which corresponds to the location
of the MSF gene. Second, results of the Northern blot analyses of
Sint1 and MSF in normal tissues are rather similar (Fig. 4)
(27), showing two predominant transcripts of 4.0 and 3.0 kb,
the 4.0 kb species being more ubiquitously expressed. In addition, a
1.7-kb transcript is seen in many human tissues, with a relatively high
level of expression in heart, liver, skeletal muscle, and kidney
(27). Finally, some minor transcripts can be detected in
tissues from both organisms. The most prominent difference in
expression pattern concerns the expression in skeletal muscle; in mice
almost no Sint1 transcripts are seen; in contrast, in humans
skeletal muscle does not seem to be different from other human tissues
regarding MSF expression. With respect to the KIAA0991 gene, the
nucleotide sequence is 100% identical to the MSF sequence in a long
continuous stretch of about 2 kb, suggesting that these two sequences
share several exons. Altogether, these observations make us incline to
the hypothesis that Sint1 represents the mouse homolog of
MSF and that MSF and KIAA0991 represent splice variants of the human
gene. Due to the similarity of expression pattern, it seems reasonable
to assume that the Sint1 cDNA clone characterized here thus
represents one of the splice variants in mice.
The genes of the septin family are considered to be involved in
cytokinesis and are characterized by a conservation of sequence motifs
defining the GTPase superfamily (3, 11). Speculations about
the mechanism of leukemogenesis involving members of this family might
thus include disturbance of the interactions with the cytoskeletal
filaments. GTP binding and hydrolysis may regulate these interactions
and/or interactions with other cell cycle proteins.
In summary, we have by a PCR screening of SL3-3-induced tumors
identified a common integration site, Sint1, and cloned a
linked septin-like gene which seems to be affected by the integrated proviruses. The assumption of a role for the Sint1 gene in
leukemogenesis is strongly supported by a recent report of a human
homolog (MSF) directly involved in a human acute myeloid leukemia as a
fusion partner at a translocation breakpoint (27). However,
since only one tumor showed an increased level of Sint1 RNA,
we must leave open the possibility of an effect of the proviral
integrations on another still not identified gene(s) at the
Sint1 locus.
 |
ACKNOWLEDGMENTS |
We thank Peder Lisby Nørby and Jesper Laursen for helpful
technical advice and discussions. Likewise, the technical assistance of
Lone Højgaard and Debra J. Gilbert is gratefully acknowledged.
This project was supported by the Danish Cancer Society, the Karen
Elise Jensen Foundation, the Danish Natural Sciences and Medical
Research Councils, the Danish Biotechnology Programme, DNA Technology
A/S, and by the National Cancer Institute, DHHS, under contract with ABL.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular and Structural Biology, University of Aarhus, C. F. Møllers Allé, Bldg. 130, DK-8000 Aarhus C, Denmark. Phone: 45 8942 3188. Fax: 45 86 196500. E-mail: fsp{at}mbio.aau.dk.
Present address: Division of Molecular Carcinogenesis, The
Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
Present address: Imperial Cancer Research Fund, Clare Hall
Laboratories, South Mimms, Hertfordshire EN6 3LD, United Kingdom.
 |
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Journal of Virology, March 2000, p. 2161-2168, Vol. 74, No. 5
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