Blood, 1 February 2002, Vol. 99, No. 3, pp. 1097-1097
CORRESPONDENCE
To the editor:
Recurrent coiled-coil motifs in NUP98 fusion partners provide a
clue to leukemogenesis
The NUP98 gene is the target of recurrent
translocations in leukemia that fuse the 5' portion of NUP98
with coding sequence from the partner gene.1-8 Three of
the known fusion partners, HOXA9, HOXD13, and
PMX1, are homeobox genes. The other known fusion partners,
DDX10, RAP1GDS1, TOP1, and
LEDGF, are considered to share no common features. Recently
NSD1, another nonhomeobox NUP98 fusion partner,
has been reported in this journal.8 We now report that the
proteins coded for by the nonhomeobox genes all have regions with a
significant probability of adopting a coiled-coil conformation.
Oligomerization via the coiled-coil domains has recently been shown to
activate the oncogenic potential of RAR
and AML1 following fusion to
partners with coiled-coil domains.9 It was shown that the
PML-RAR, PLZF-RAR, NPM-RAR, and AML1-ETO fusion proteins each
exist in oligomeric complexes in vivo and that oligomerization causes
abnormal recruitment of the transcriptional corepressor N-CoR.
Moreover, fusion of RAR to the oligomerization domain of p53 showed
that oligomerization alone is sufficient for transformation. Other
leukemia fusion genes also involve the fusion of transcription factors
with genes coding for coiled-coil domains. For example, the
inv(16)(p13q22) fuses the N-terminus of CBF
with the C-terminus of
the smooth muscle myosin heavy-chain gene.10 The
coiled-coils of the myosin heavy-chain gene promote dimerization and
are essential for the transforming properties of the fusion
gene.11
Coiled-coils are characterized by sequence patterns known as heptad
repeats, which result in the formation of amphipathic alpha helices,
the hydrophobic faces of which undergo what is known as
"knobs-into-holes packing" as first proposed by
Crick.12 Potential coiled-coil forming sequences were
sought using both algorithms in COILS 2.1 (http://www.ch.embnet.org/software/COILS_form.html). The original
algorithm of Lupas et al gives equal weighting to each of the 7 heptad
positions in its scoring of coiled-coil potential.13 This
weighting system is biased toward hydrophilic charge rich sequences and
can occasionally give rise to false positive coiled-coil predictions
where there is no heptad periodicity. The revised algorithm increases
the weighting of positions a and d, which code for hydrophobic amino
acids, thereby decreasing scores for segments with a high number of
charged residues and reducing false positive
predictions.14
The protein sequences analyzed were DDX10 (PID g13514831), smgGDS, the
product of RAP1GDS1 (PID g7239381), TOP1 (PID g13653668), LEDGF (PID g11360305), and NSD1 (PID g15213542). All proteins were
predicted to form coiled-coils even when the weighting of positions a
and d was increased. This contrasts with proteins in general where it
is considered that 3% to 5% have potential coiled-coil
domains.15 The potential coiled-coil domains were identified in DDX10 at Asn579-Lys600 (P = .59), smgGDS at
Thr425-Glu452 (P = .66), and Ile505-Leu533
(P = .86), TOP1 at Lys310-Tyr338 (P = .59),
Leu577-Leu605 (P = .54), and Lys638-Thr718
(P = 1.0), LEDGF at Lys309-Glu331
(P = .71) and Val370-Glu395 (P = .98), and
NSD1 at Gly1729-Asn1760 (P = .96). The SOPM
(self-optimized prediction method) secondary structure prediction
program
(http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopm.html) showed that all the putative coiled-coil sequences were predicted to
form alpha helices. Furthermore, the predicted coiled-coil domain
at Lys638-Thr718 of TOP1 has been verified by x-ray
crystallography.16
In all cases of fusion with NUP98, the predicted coiled-coil domains
are retained in the fusion protein. Thus translocations not
involving homeobox genes result in the fusion of an amino-acid sequence
with coiled-coil forming potential to the FG-repeat-rich amino
terminus of NUP98. It has been shown that this FG-repeat region of
NUP98 possesses strong transcriptional transactivation potential
through direct interaction with CBP/p300.17 Another FG-repeat-containing nucleoporin gene, NUP214, is also
involved in recurrent leukemia translocations. These involve fusion of NUP214 FG repeats to the SET protein or the DEK
protein.18,19 Significantly, COILS 2.1 analysis shows that
the portions of SET (PID g14745487) and DEK (PID g544150) retained in
NUP214 fusions have a region with high coiled-coil forming potential
(SET Lys35-Gln78 [P = .99] and DEK Glu323-Val350
[P = .92]). Interestingly, none of the 3 homeobox
proteins fused to NUP98 in AML are predicted to form
coiled-coils when analyzed with COILS 2.1. This probably reflects a
different mode of action of the homeobox transcription factors and
suggests that NUP98-homeobox fusions have a different mechanism of leukemogenesis.
It is a matter of speculation whether these coiled-coil regions promote
self-dimerization/oligomerization or have a role in formation of
multimeric complexes, which facilitate interaction with other
transcription factors or cofactors. The latter may be more likely since
2 of the nonhomeobox fusion partners, LEDGF and NSD1, are known
transcription factors. The exact significance of the coiled-coil
structure in all reported nonhomeobox NUP98 fusion partners requires
further research and may give a clue to the pathogenesis of NUP98
fusion proteins.
Acknowledgements. We thank Andrei Lupas from the Max Planck
Institute for Developmental Biology, Tübingen, Germany, for
advice on the use of COILS 2.1. We thank John Walshaw from the School of Biological Sciences, University of Sussex, United Kingdom, for
commenting on COILS 2.1 predictions presented here and for helpful
discussion. We thank Sally Stephenson and Chris Slape for reading the manuscript.
Damian James Hussey and Alexander Dobrovic
Correspondence: Damian James Hussey, Department of
Haematology-Oncology, The Queen Elizabeth Hospital, Woodville, SA 5011, Australia; e-mail: damian.hussey{at}adelaide.edu.au
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