The Dkk3 gene encodes a vital intracellular regulator of cell proliferation
The Dkk3 gene encodes a vital intracellular regulator of cell proliferation
Jack L. Leonard 0 1 2 3
Deborah M. Leonard 0 1 3
Scot A. Wolfe 0 1 3
Jilin Liu 0 1 3
Jaime Rivera 0 1 3
Michelle Yang 0 1 3
Ryan T. Leonard 0 1 2 3
Jacob P. S. Johnson 0 1 3
Prashant Kumar 0 1 3
Kate L. Liebmann 0 1 2 3
Amanda A. Tutto 0 1 2 3
Zhongming Mou 0 1 2 3
Karl J. Simin 0 1 3
0 a Current address: Validars, Worcester, Massachusetts, United States of America ¤b Current address: University of Vermont Medical College , Burlington , Vermont, United States of America ¤c Current address: Institute of Bioinformatics , Karnataka , India
1 Institutes of Health NIDDK: DK38772 and DK060051 to J.L.L., Pancreatic Cancer Alliance Fund (
2 Department of Microbiology and Physiological Systems, University of Massachusetts Medical School , Worcester , Massachusetts, United States of America, 2 Program in Molecular Medicine, University of Massachusetts Medical School , Worcester , Massachusetts, United States of America, 3 Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester , Massachusetts, United States of America, 4 Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester , Massachusetts, United States of America, 5 Department of Cell and Molecular Physiology, University of Massachusetts Medical School , Worcester , Massachusetts, United States of America, 6 Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts , United States of America
3 Editor: Irina U Agoulnik, Florida International University , UNITED STATES
Members of the Dickkopf (Dkk) family of Wnt antagonists interrupt Wnt-induced receptor assembly and participate in axial patterning and cell fate determination. One family member, DKK3, does not block Wnt receptor activation. Loss of Dkk3 expression in cancer is associated with hyperproliferation and dysregulated û-catenin signaling, and ectopic expression of Dkk3 halts cancer growth. The molecular events mediating the DKK3-dependent arrest of û-catenin-driven cell proliferation in cancer cells are unknown. Here we report the identification of a new intracellular gene product originating from the Dkk3 locus. This Dkk3b transcript originates from a second transcriptional start site located in intron 2 of the Dkk3 gene. It is essential for early mouse development and is a newly recognized regulator of û-catenin signaling and cell proliferation. Dkk3b interrupts nuclear translocation û-catenin by capturing cytoplasmic, unphosphorylated û-catenin in an extra-nuclear complex with û-TrCP. These data reveal a new regulator of one of the most studied signal transduction pathways in metazoans and provides a novel, completely untapped therapeutic target for silencing the aberrant û-catenin signaling that drives hyperproliferation in many cancers.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information
The Dickkopf family of secreted glycoproteins is composed of four members that first
appeared in early metazoans as key regulators of the Wnt/û-catenin signaling pathway [1±4].
Three family members DKK1, DKK2 and DKK4 bind to the LRP5/6 and Kremen subunits of
the receptor [
] and prevent assembly of a functional Wnt receptor complex [6±8]. The
following competing interests: Jack L. Leonard,
Deborah M. Leonard and Karl J. Simin and the
University of Massachusetts Medical School have a
patent pending PCT/US2013/031118 entitled
ªAntitumor Properties of Dickkopf 3bº; Jack L. Leonard
claims ownership of stocks and shares in Acworth
Pharmaceuticals, Inc. and is a consultant for
Acworth Pharmaceuticals, Inc. with interests in the
DKK3b protein. This does not alter our adherence
to PLOS ONE policies on sharing data and
remaining family member, DKK3, apparently evolved divergently [
] and does not bind to
LRP5/6 or modulate Wnt receptor assembly/signaling [10±13], even though it retains the two
cysteine rich domains common to all family members . Despite its inability to disrupt Wnt
receptor binding, DKK3 is the best-known tumor suppressor in the family [
expression is frequently silenced in cancer, often by the hyper-methylation of CpG islands
located in the Dkk3 locus [13±15] and ectopic over-expression of DKK3 slows û-catenin driven
cancer cell proliferation in vitro [16±19]. To date, the molecular details of the mechanism
DKK3 action remain elusive. Despite its presumed role in regulating û-catenin driven cancer
cell proliferation, targeted inactivation of the mouse Dkk3 gene failed to provide a direct link
between DKK3, the Wnt/û-catenin signaling, and control of cell proliferation. The Dkk3tm1Cni
mutant mouse is viable, fertile, shows no û-catenin signaling defects or any increase in cancer
susceptibility  and failed to phenocopy other Dickkopf deletion mutants [21±25] or
deletion mutants of individual components the Wnt/û-catenin pathway [26±32].
In this study, we show that the Dkk3 gene encodes a second vital intracellular isoform,
DKK3b, that inhibits hyperproliferation in cancer cells by blocking the û-catenin nuclear
translocation downstream of the Wnt-regulated û-catenin destruction complex. In normal
mouse fibroblasts, loss of DKK3b disrupts cell adhesion. This newly discovered Dkk3 gene
product is an obligatory negative regulatory element in the û-catenin signaling axis that adds a
non-canonical attenuating mechanism to one of the most studied signal transduction
pathways in metazoan systems. DKK3b captures û-catenin in an extra nuclear complex with
ûTrCP preventing its nuclear translocation and serving as a gatekeeper for û-catenin nuclear
entry that modulates û-catenin-dependent gene expression.
Materials and methods
Pregnant Sprague Dawley rats were purchased from Charles-River Labs. C57Bl/6J and CD1
mice were obtained from Jackson Labs and Charles River respectively. All rodents used in this
study were maintained in an AALAC-accredited facility. The Animal Care and Use Committee
of the University of Massachusetts Medical School (Assurance #A3306-01) approved the use of
animals. All rodents were euthanized by CO2 asphyxiation followed by decapitation. Frozen
whole brain from homozygous and heterozygous Dkk3tm1Cni were the gift of Dr. C. Niehrs.
Generation of Dkk3CFP mutant mice
Zinc Finger Nuclease (ZFN) target sites within intron 2 of mouse Dkk3 gene (NCBI:
NC_000073.6) were identified (nt8312-nt8341: AGCCCCTTTTCttcacctCAGTTGTAACTG)
] and two four finger nucleases were assembled. The cDNAs encoding the zinc fingers
were generated by gene synthesis (IDT) and then cloned into a pCS2 expression vector bearing
the heterodimeric DD and RR versions of FokI : The complete amino acid sequences of
the ZFNs are 5’ HA-ZFN (5’-GAAAAGGGGCT; DD FokI): NH2 YPYDVPDYATERPYKCP
GAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF-COOH and the 3’ Flag-ZFN (5’-CA
GTTGTAACTG; DD FokI): NH2-DYKDDDKTERPYKCPECGKSFSRSDTLV
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homologous recombination donor DNA for the mouse target Dkk3 locus was assembled by PCR
amplification. PCR primers are listed in (Table 1).
The 824 bp 5' homology arm (nt7415-nt8239) and 722 bp 3'homology arm (nt8342-nt9064)
were appended to a loxP-TagCFP-pA-loxP cassette to create a linear 2.7 kb Dkk3b HR Donor
DNA ZFN and HR Donor DNA. Validation was performed in the C8D1A cells (ATCC)
derived from the C57Bl/6J mouse cerebellum. C8D1A cells were transfected with Dkk3
targeted ZFN plasmids and genomic DNA was isolated 48 h later. The 681 bp target locus was
PCR amplified, heat denatured, re-annealed and indel formation evaluated by Cel-1 assay [
(Transgenomic, Inc.). HR repair of the ZFN generated DSB was validated using ssDNA
oligonucleotides to insert a unique restriction site at the DSB [
]. C8D1A cells were transfected
with a 96-mer ssDNA oligo with a unique EcoRI site bracketed by 45 nt long homology arms
GAAAGAAACCGTTTGTGTCTTTGATTTGATAGATG) along with the Dkk3 targeted ZFN
plasmids using Fugene6. The Dkk3 target sequence was PCR amplified from gDNA isolated 48 h
after transfection. HR mediated repair of the ZFN generated DSB was confirmed by the EcoRI
restriction of the PCR amplified target sequence.
Capped, polyadenylated ZFN mRNAs were synthesized in vitro (Ambion), purified
(Qiagen) and injected along with the 2.7 kb linear Dkk3b HR Donor DNA into the nucleus and
cytoplasm of C57Bl/6J zygotes (UMMS Transgenic Core). Injected zygotes were implanted
into the uteri of pseudo-pregnant C57Bl/6J dams and gene edited pups were identified by
genotyping (see Fig 1A and Table 1 for genotyping primer pairs: DPF1:DPR2, mut-407 bp; D3F3:
D3R4, mut-1031 bp; DPF1:D3R4, wt-618 bp, mut-1747bp). Insertion of the CFP cDNA at the
target locus was confirmed by DNA sequencing of PCR products generated with primers LL
(nt7259-nt7284) and RR (nt9058-nt9027) located 166 nt and 444 nt respectively, outside the
Predicted off-target sites were identified by PROGNOS [
]. Potential off-target sites were
PCR amplified from liver gDNA (founder #19) and cloned into the pCR4 vector (Life
Technologies). Eight to twelve independent clones of each potential off-target site were DNA
sequenced in both directions.
The transcription initiation site in exon 2 of the mouse Dkk3 gene was captured by 5'RACE
of mRNA purified from the mutant mouse Dkk3CFP cerebral cortex using the SMARTer1
RACE 5'/3' kit from Clontech laboratories following manufacturer's instructions. Briefly,
mRNA was purified using the Dynabeads1 mRNA Direct™Kit from ThermoFisher according
to manufacturer's instructions. Mouse brain mRNA (500 ng) was used for 1st cDNA synthesis
and the 5'UTR of the Cfp mRNA was amplified from the 1st strand cDNA by 5'RACE PCR
using the kit upstream UPM primer (5’-GTAATACGACTCACTATAGGGCAAGCAGTGGTAT
CAACGCAGAGT) and two, independent, Cfp-specific downstream primers each with an
appended infusion cloning sequence (bolded nucleotides): one located 384 nucleotides
downstream from the Cfp ATG start site CFP384R (5’-gattacgccaagcttCTCGCCCTTCAGC
TCGACGCGGTTCACC) and a second located 234 nucleotides downstream of the Cfp ATG start
site CFP234R (5’- gattacgccaagcttCATGTGCTCGGGGTAGCGGGCGAAGC). Specific
PCR products of ~500 bp and ~300 bp, respectively, were gel isolated, cloned into the pRACE
vector (TaKaRa) and 15 clones from each Cfp primer were DNA sequenced.
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Fig 1. Identification of multiple transcripts originating for the Dkk3 gene locus. (A) Schematic diagram
of the Dkk3 gene (NC_000073.6) in the wild type and Dkk3tm1Cni mouse. Initiator methionine's for Dkk3
(NM_0154814) and D2p29 (AF245040) indicated by arrows; CpG islands indicated by red box; LacZ-pA stop
cassette in yellow. (B) Quantitative PCR of Dkk3 containing exon 2 and exon 3 transcripts in total brain RNA
from the Dkk3tm1Cni mouse. Arrows indicate PCR primer sites. Data reported as means ± se of 3 individuals;
each sample determined in quadruplicate. (C) Schematic diagram of rat Dkk3 intron 2-luciferase reporter
constructs. Arrows indicate orientation and location of intron 2 segments upstream of exon 3; data reported as
means ± se of 3 independent experiments, each sample determined in triplicate. (D) ChIP analysis of RNA pol
II and TATA box binding protein (TBP) binding to the ~66 nucleotides (nt6682-nt6948) of intron 2 adjacent to
exon 3 in the rat astrocyte Dkk3 gene; data reported as means ± se of 3 independent experiments; each
sample determined in quadruplicate.
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Cell culture and transfection
Primary astrocytes were prepared from one-day-old neonatal rat or mouse [
embryonic fibroblasts (MEFs) were prepared from 13.5±14.5 day old fetuses [
]. Cells were
maintained at 37ÊC under 5% CO2 in Dulbecco's modified Eagle's medium (DMEM)
containing 10% bovine calf serum (BCS), 50 units/ml penicillin, 90 units/ml streptomycin. All cell
cultures were passaged every 5±7 days for up to 3 passages.
PC3, HEK293, HeLa and C8D1A cells were maintained in DMEM supplemented with 25
mM HEPES (pH 7.4) 10% fetal bovine serum, 100 units/ml penicillin, 100 μg/ml streptomycin
and 2 mM L-glutamine. Cells were seeded at a density of 15,000 cells/cm2 24 h prior to
Transient transfections were done with Fugene6 according to manufacturer's instructions.
Cell lysates were prepared 48 h after transfection. Each transfection experiment repeated at
least 3 times and each assay point was determined in triplicate.
Tunable ectopic protein(s) expression was done using the Tet-ON expression system (Life
Technologies). The Tet Repressor Protein (TR) was integrated in the genome of PC3 cells by
lentivirus infection (pLenti3.3/TR, Life Technologies) and cell selected with G418. TR
expressing PC3 cells were transfected with pTREX-DKK3-HA or pTREX-Flag-IBS and ectopic
protein expression induced by addition of increasing concentrations of doxycycline to the growth
Luciferase reporter assays
Promoter analysis was done with PCR isolated segments of intron 2 of the rat Dkk3 gene. The
Tcf promoter [
] (M50 Super 8x TOPflash) was a gift from Randall Moon (Addgene plasmid
# 12456)); the E-Cad promoter [
] was a gift from Eric Fearon (Addgene plasmid # 19290));
and the E2F promoter[
] was the gift of Jason Chen. All promoter cDNAs were cloned into
the pGL4 firefly luciferase vector (Promega). Cells were transfected with the individual
promoter-reporter plasmids using Fugene6. After 48 h, cell lysates were prepared and luciferase
assays were done according to manufacturer's instructions (Promega). û-catenin signaling was
evaluated in cells co-transfected with the Wnt expression plasmid, pcDNA-Wnt1 [
pcDNA-Wnt1 was a gift from Marian Waterman (Addgene plasmid # 35905). Each
promoterreporter experiment was performed in triplicate, and each experiment was repeated at least
Chromatin immunoprecipitation (ChIP) was done as described [
] with modifications.
Primary rat astrocytes were cross-linked with 1% formaldehyde. Washed cell pellets were lysed
on ice in hypo-osmotic lysis buffer, nuclei collected by centrifugation, and DNA sheared
(average size 200±400 bp) by sonication in iso-osmotic sonication buffer. Clarified extracts were
pre-cleared with A/G plus-agarose beads pre-coated with 2 μg/ml sonicated salmon sperm
DNA and 1 mg/ml bovine serum albumin. Thirty A260 units of the pre-cleared nuclear lysate
was then incubated with 3 μg of anti-RNA pol II, anti-TBP or normal Rabbit IgG and immune
complexes isolated by A/G plus-agarose beads (Santa Cruz Biotech.). Immune complexes were
eluted in 50 mM Tris, pH 8, 1 mM EDTA, 1% (v/v) SDS at 65ÊC for 15 min, adjusted to 200
mM NaCl, and cross-links broken by heating at 65ÊC for 16 h. Immune complexes were then
treated with RNase I (1 unit/ml) and Proteinase K (20 μg/ml) and DNA purified (Qiagen).
Immune-precipitated DNA and input DNA (10% total) were analyzed by real time PCR (MJ
Research Thermal Cycler) using the SYBR Green PCR kit (Qiagen) and primers TSS2F and
TSS2R (Table 1). μ
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Cells were seeded onto on poly-d-lysine (10 μg/ml) coated coverslips and grown for 24 h prior
to transfection. All transfections were done with Fugene6 according to manufacturer's
instructions. After 48 h, cells were washed with ice cold PBS, fixed with 4% paraformaldehyde in PBS
for 10 minutes and quenched with 10 mM glycine. Fixed cells were permeabilized with Triton
X-100, blocked with 1% BSA in TRIS buffered saline containing 0.1% Tween 20 and then
incubated with primary antibodies (0.2±1 μg/ml) for 1 h at room temperature. After washing,
immune complexes were visualized with secondary antibody-Alexafluor conjugates for 1 h.
Nuclei were stained with DAPI. Coverslips were mounted with Prolong1 Gold mountant
(ThermoFisher). Tissue sections (5 μm) were prepared by the Morphology Core (UMMS)
from paraffin embedded, formalin fixed organs from a Dkk3CFP/+ mutant mouse. Dewaxed
sections were stained with anti-CFP antibody (1 μg/ml) and counter stained with hematoxylin
and eosin. Antibodies used in this study were: anti-HA (ab1424), anti- û-tubulin (ab6046),
anti-DKK3 (ab186409) (Abcam), anti-FLAG (M2; F3165), anti-Myc (SAB4300320)
anti-ûcatenin (04±958) (Sigma), anti-CFP (cat#632381) (TaKaRa), anti-û-TrCP (mAB #4394),
antiGAPDH (mAB #2118) (Cell Signaling), and anti-Dkk3b [
]. Alexfluor488 and Alexafluor568
conjugated and HRP-conjugated secondary IgGs (cat#: A-11008, A-11034, A-11004, A11036,
31430, 31460) were purchased from Life Technologies; RDye680CW and IRDye800CW
conjugated secondary IgGs (cat#: 925±68020, 925±68022, 925±32210, 925-32211were purchased
from Li-COR Biosciences.
MEFs were infected with pools of lentiviral shRNAs in pGIPZ from (Dharmacon) archived by
UMMS RNAi Core. Lentiviral pools of shRNAs (>1 x 106 pfu/ml per shRNA target) targeting
the open reading frame of mouse DKK3 and Dkk3b transcripts (exons 4 and 8)
(V3LMM_518668, V3LMM_487209, V3LMM_487206, V3LMM_487207), mouse û-catenin
(exons 5 and 8) (V2LMM_16708, V3LMM_491202, V2LMM_4912040), and human û-TrCP
(V2LHS_33325, V2LHS_33330, V2LHS_33325) and a non-silencing control (RHS4348) were
used. Cells were infected with lentiviral pools of shRNAs (>1 x 106 pfu/ml per shRNA target),
grown for 2 days and selected with puromycin. GFP positive shRNA expressing cells were
used in all experiments.
Total RNA isolation, and real time PCR
Total cellular RNA was isolated using Trizol Reagent (Life Technologies) or RNeasy (Qiagen)
according to the manufacturer instructions. RT-PCR was performed with SuperScript
FirstStrand Synthesis System (Life Technologies) and primed with either Oligo(dT) or random
hexamers. First strand cDNAs primed with either Oligo(dT) or random hexamers yielded
identical results. Initially, real time PCR (MJ Research Thermal Cycler) was done with a SYBR
Green PCR kit (Qiagen). All subsequent experiments were done using multiplexed TaqMan1
Probes and the VIIA Real Time PCR System (Applied Biosystems). TaqMan1 Fast Advanced
Master Mix and taqMan1 probes for mus Dkk3 exons 1±2, Mm01269624; mus Dkk3 exons
3±4, Mm00443801; mus Cyclin D1; Mm00432359; mus c-Myc, Mm00487804; human Cyclin
D1, Hs00765553; human c-Myc, Hs00153408; human Axin2, Hs00610344; human Cox2,
Hs000153133; human Wfdc2, Hs00899484; human Cdh2, Hs00983056; human; human Fosl1,
Hs04187685; human, Tuba, Hs0102675; and human Gapdh, Hs03929097 were purchased
from Life Technologies.
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Co-immunoprecipitation binding studies
Cells expressing the epitope-tagged target proteins were lysed in 1X IP buffer (ThermoFisher
Sci) with 150 mM NaCl, protease and phosphatase inhibitors. Lysates were incubated with
anti-epitope antibody for 3 hrs at 4ÊC and immune complexes collected on
ProteinA/G-agarose beads (Sigma). Immune complexes were washed five times with lysis buffer and eluted in
Laemmli buffer containing 1% SDS. Cell extracts and immune complexes were separated by
SDS±PAGE and immunoblot analysis done with anti-Flag, anti-Myc and anti-HA antibodies.
Native û-catenin and û-TrCP in HeLa cells were co-immunoprecipitated from cells treated
for increasing times with TAT-Dkk3b. Anti-Dkk3b affinity DynaBeads1 (7.2 μg/mg resin)
and control rabbit IgG affinity DynaBeads1 (8.4 μg/mg resin) were prepared by coupling
affinity purified anti-Dkk3b IgG [
] and rabbit IgG, respectively, to Dynabeads M-270
(ThermoFisher) according to manufacturer's instructions. HeLa cell lysates were prepared in 1X IP
buffer (ThermoFisher) supplemented with 150 mM NaCl and 1X protease inhibitors. Cell
lysates (200 μg protein) were incubated with 1 mg of anti-Dkk3b or Control affinity beads, in
duplicate. Immune complexes were collected using a DynaMag™magnet. Acid eluates were
then separated on 10% SDS-PAGE gels and target proteins identified by immunoblot. All
native co-immunoprecipitation experiments were repeated three times.
TAT-fusion protein synthesis
Dkk3b cDNA was cloned into the pTAT-HA plasmid [
], a gift from Steven Dowdy
(Addgene plasmid # 35612). TAT-Dkk3b expression was induced with isopropyl
û-D-1-thiogalactopyranoside in BL21(DE3) cells. TAT-Dkk3b present in inclusion bodies was solubilized
by denaturation in PBS containing 6 M urea, purified by affinity chromatography on Ni-NTA
resin, and eluted with 150 mM imidazole in 6M Urea. Urea was rapidly removed by G10 spin
column gel filtration and TAT- Dkk3b was stored at -20ÊC at 1 mg/ml in PBS at pH 6.0.
The Dkk3 gene encodes multiple transcripts
The unaltered û-catenin signaling in the Dkk3 knockout mouse (Dkk3tm1Cni)  led us to re
examine the biological relevance of an intracellular ~30 kDa DKK3 isoform (D2p29) that
showed dynamic, microfilament dependent intracellular trafficking in rat astrocytes [
Amino acid sequence alignment showed that the secreted DKK3 and D2p29 (designated
hereafter Dkk3b) shared all but the N-terminal 71 residues that comprise the signal peptide
sequence and N-glycosylation sites.
The Dkk3tm1Cni mutant mouse was generated by replacement of the majority of exon 2 of
the Dkk3 gene with an in-frame LacZ-stop cassette [
]. Exon 2 encodes the N-terminal 71
amino acids responsible for directing DKK3 to the secretory vesicle, and also harbors a
biologically important CpG island (Fig 1A).
The first codon in exon 3 of the Dkk3 gene encodes the initiator methionine of Dkk3b from
frogs to man, suggesting that Dkk3b is generated from a second Dkk3b transcript, possibly
initiating within the 6 kb intron 2 (Fig 1A). Using exon specific qPCR to quantify Dkk3 locus
transcripts containing exon 2 or exon 3 (Fig 1B, S1 Fig), we found that all Dkk3 transcripts
present in mouse astrocyte mRNA had Dkk3 exon 3 codons, while only ~60% generated a
PCR product with Dkk3 exon 2 specific PCR primers, suggesting that ~40% of the total Dkk3
mRNA lacked the exon 2 codon and could presumably encode Dkk3b (S1 Fig). The specificity
of the exon-specific qPCR of these Dkk3 exons was validated using total RNA from Dkk3tm1Cni
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mutant mouse brain; no Dkk3 transcripts with exon 2 codons were detected and only Dkk3
transcripts with exon 3 codons were found (Fig 1B).
Promoter: luciferase reporter assays were used to search for transcriptional regulatory
elements located in intron 2 of the rat Dkk3 gene. Robust promoter activity is found in the 750
nucleotides of intron 2 immediately upstream of exon 3 and progressive deletion from the 5'
end of this intron 2 fragment localized a functional promoter (TSS2) to the 250 nucleotides
just upstream of the 5' end of exon 3 (Fig 1C). The essential TATA box was located at -35
nucleotides upstream from the 5' end of exon 3 of the Dkk3 gene (Fig 1C, see construct
P259D); in mouse and human Dkk3 genes a TATA box is located ~90 nucleotides upstream of
exon 3 and the transcriptional start site was determined to be at -92 nucleotides upstream of
exon 3 by 5'RACE analysis of the Cfp mRNA surrogate of DKK3b (see S2 Fig). Chromatin
immunoprecipitation (ChIP) of rat astrocyte gDNA revealed that the native TSS2 in the Dkk3
gene bound RNA pol II (Fig 1D) and the TATA Box Binding Protein (TBP) (Fig 1D)
indicating that the TATA box at -35nt in intron 2 (see Fig 1C) is functional.
Dkk3b is a biologically active product of the Dkk3 gene in vivo
To explore the biological significance of Dkk3b, we used targeted homologous recombination
(HR) driven by artificial nucleases to selectively disrupt this transcript within the mouse
genome. A promoter trap knock-in strategy was devised using zinc finger nucleases [
(ZFNs) to create a double stranded break (DSB) in intron 2 of the Dkk3 gene between TSS2
and exon 3 that would facilitate the HR mediated insertion of a floxed CFP-stop cassette. Splice
junctions at exon 3 were preserved so that TSS1-driven transcripts encoding the secreted
DKK3 could produce full-length, spliced mRNA (Fig 2A±2C). The CFP insert diverts
TSS2-driven transcription to the CFP surrogate resulting in the selective, functional loss of
Dkk3b transcripts in homozygous animals. Immortal C8D1A cells, isogenic to the C57Bl/6j
mouse, Cel-I assays, and single stranded oligonucleotide directed HR repair were used to
validate the targeting strategy and ZFN-facilitated donor DNA HR. ZFN-generated DSBs and HR
repair in the presence of the donor DNA resulted in weak expression of CFP in C8D1A cells
(Fig 3A). These modified cells retain an intact exon 2 CpG island(s) upstream of the edited
Dkk3 locus [49±51]. Since CpG island methylation is common in immortalized cells [
presumably depresses expression of REIC (Reduced Expression in Immortal Cells)Ða
synonym for DKK3 [
]Ðwe examined whether the methyltransferase inhibitor, azacytidine,
would enhance expression of the TSS2-driven CFP decoy. Inhibition of DNA
methyltransferase activity in the gene-edited C8D1Acfp/wt cells resulted in a >5-fold increase in CFP
expression (Fig 3A).
C57Bl6 mouse zygotes were then injected with ZFNDkk3b mRNAs and a linear HR donor
DNA to create the Dkk3bCFP knock-in mouse. Thirty-five of 65 (54%) injected one cell
embryos produced viable pups, and DNA sequencing of the target locus confirmed that 1 male
(#17) and 2 females (#18 & #19) (8.6%) had HR mediated insertion of a floxed CFP decoy
inserted 35 nucleotides upstream from exon 3 (see Fig 2C) with intact splice junctions. No
offtarget mutations were found for the 10 highest predicted candidate target sites in founder #19
(Table 2). F1 progeny from crosses of the Dkkb3CFP/+ male and a wild type female showed
Mendelian inheritance patterns characteristic of a single segregating allele (Table 3). The tissue
distribution of Dkk3b expression was evaluated using the ~26 kDa CFP surrogate in the
Dkk3bCFP/+ mutant mouse. Immunoreactive CFP was found throughout the Dkk3bCFP/+
mouse (Fig 3D) illustrating the ubiquitous nature of TSS2 activity of the Dkk3 gene.
The mRNA for the CFP surrogate of Dkk3b was then used to establish the TSS2-driven
transcription initiation site by 5'RACE of polyadenylated mRNA isolated from the cerebral
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Fig 2. Targeting strategy for ZFN gene-editing of the Dkk3b locus in the mouse. (A) Organization of
exons 2±4 of the wild type Dkk3 locus. TSS1, transcriptional start site 1; TSS2, transcriptional start site 2 and
ZFN targeting site. (B) Organization of the HR donor. C. Schematic diagram of the gene edited Dkk3bCFP
locus. Target locus modification confirmed using PCR primers anchored outside of the HR region (LF and RR)
and overlapping in the CFP cds (LR and RF). PCR products (LF:LR and RF:RR) were sequenced in both
directions. Genotyping PCR primers indicated by arrows (see Table 1 for sequences).
cortex of the mutant Dkk3CFP mouse. The Cfp mRNA began at nt8284 of the Dkk3 gene, ~90
nt upstream of the ATG start site of exon 3 of the Dkk3 gene (S2 Fig). The 5'UTR of the Cfp
transcript also harbored the imbedded LoxP site used to excise the promoter trap reporter
illustrating that the TSS2 is functional at this mouse gene locus.
No viable homozygous mutant offspring were found after mating of heterozygous
Dkk3bCFP/wt mice (Table 3), and no homozygous mutant blastocyst implants were found as
early as embryonic day 5.5 (n = 34 embryos) suggesting that DKK3b is essential for
development at or near the time of embryo implantation. This outcome differs markedly from that of
the Dkk3tm1Cni mouse and suggests that at least one wild type Dkk3b allele is required for
survival. The penetrance of the lethal phenotype for the single segregating Dkk3bCFP allele was
confirmed in out-crosses on the CD1 background (Table 3).
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Fig 3. Analysis of the biological role the TSS2 driven Dkk3b in the ZFN gene-edited Dkk3bCFP/+
mouse. (A) Inhibition of DNA methyltransferase activity increases TSS2-driven CFP in Dkk3bCFP/+ cells. (B)
DKK3 isoforms present in wild type and Dkk3bCFP/mCherry MEFs (anti-DKK3 (ab186409) (Abcam). (C) QPCR
analysis of Dkk3 and Dkk3b transcripts in wild type and Dkk3bCFP/mCherry MEFs. Data reported as means ± se,
n = 3. (D) TSS2-driven, immunoreactive CFP expression in representative tissues of the Dkk3bCFP/wt mouse.
NSB, Normal rabbit serum, CFP, anti-CFP IgG(cat#632381) (TakaRa).
Excision of the floxed CFP cassette (ΔCFP) in the unfertilized mutant oocyte using a Sox2
promoter-driven Cre recombinase [
] rescued the lethal phenotype of the Dkk3bCFP
mutation and left behind a diagnostic single 34 bp loxP remnant at the target locus. Bi-allelic,
gene-edited Dkk3bΔCFP/CFP offspring were recovered from crosses of Dkk3bΔCFP/+ to a
Dkk3bCFP/+ mice (Table 3) and showed Mendelian inheritance confirming that embryonic
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lethality resulted from the interruption of Dkk3b transcription rather than any tightly linked
cis gene defect(s).
Since embryonic lethality prevented the generation of homozygous mutants, ex vivo gene
editing of heterozygous mutant MEFs was used to confirm the promoter trap knock-in
strategy. Bi-allelic disruption of the Dkk3b locus was done in heterozygous mutant MEFs
(Dkk3bCFP/+) using a second round of ZFN-initiated, HR repair to insert an mCherry reporter
into the remaining wild type allele. Forty-eight hours after ex vivo gene editing, viable MEFs
with bi-allelic mutations at the target locus expressing both fluorescent proteins were found
attached to the dish, as well as free floating in the growth medium. Mutant Dkk3bCFP/mCherry
MEFs, both attached and free floating, were pooled and sorted by FACS. Immunoblots of
sorted cell lysates showed that the Dkk3bCFP/mCherry MEFs continued to express the ~65 kDa
glycosylated DKK3 protein, while the 30 kDa DKK3b was absent (Fig 3B). Exon-specific qPCR
confirmed preservation of the secreted Dkk3 transcript and the selective loss of the Dkk3b
transcript in Dkk3bCFP/mCherry MEFs (Fig 3C). Attempts to propagate these mutant MEFs was
prevented by the severe attachment defect associated with the DKK3b-deficient cells. These data
suggest that DKK3b is necessary for cell-cell interactions, required for embryogenesis, and that
TSS2-driven CFP is a surrogate for Dkk3b expression.
RNAi knock down was used to explore the role of DKK3b on MEF attachment, cell
proliferation and its relationship to û-catenin signaling. RNAi knockdown of the Dkk3/Dkk3b and/or
ß-catenin transcripts in MEFs was confirmed by qPCR (Fig 4A). The effects of Dkk3b
knockdown on û-catenin dependent gene expression was examined using the û-catenin responsive
TOPflash luciferase reporter. Dkk3b KD MEFs showed a 10-fold increase in basal TOPflash
activity compared that of the unaltered control and non-silencing KD cells (Fig 4B).
Simultaneous knockdown of Dkk3/Dkk3b and ß-catenin expression completely blocked this increased
signaling. Similar to the Dkk3b-null MEFs (see above), >70% of the viable Dkk3/Dkk3b KD
cells were found free-floating after 3 days in culture (Fig 4C). Cell attachment and proliferation
during this 3-day growth period was unaffected in cells expressing a non-silencing shRNA
control or in ß-catenin KD cells (Fig 4D). The attachment defect in Dkk3/Dkk3b KD cells was
completely reversed by simultaneous knockdown of ß-catenin mRNA (Fig 4D and 4E).
Replacement of cellular DKK3b by addition of a cell penetrating TAT-DKK3b protein to the
growth medium [
] completely restored cell attachment of the Dkk3/Dkk3b knockdown
MEFs to that of the controls, but provided no additional benefit to either the ß-catenin KD
cells or in ß-catenin KD:Dkk3/Dkk3b KD MEFs (Fig 4D and 4E).
DKK3b modulates cell proliferation and û-catenin signaling
The relationship between DKK3b and the û-catenin signaling pathway was further defined by
cell proliferation, promoter-driven reporter assays, and cell migration analysis in prostate and
breast cancer cells. Tet-inducible constructs of the intracellular DKK3b and the secreted
DKK3 were used to provide fine control over exogenous expression levels and to avoid the
untoward effects of over-expression. In the DKK3/DKK3b-deficient, PC3 prostate cancer line,
expression of DKK3b arrested cell proliferation of the (Fig 5A) at the G0/G1 phase of the cell
cycle (Fig 5B) and led to the loss of DKK3b expressing cells by 24±36 h of induction (Fig 5A).
Unlike prior over-expression studies [
11, 19, 56, 57
], induction of equivalent levels of secreted
DKK3 did not alter PC3 cell proliferation (Fig 5A and 5B).
These data show that DKK3b has the anti-proliferative activity in cancer cells that were
previously associated with gene product(s) from the Dkk3 locus [
The relationship between DKK3b and û-catenin signaling was defined by cell proliferation
and promoter-driven reporter assays in HEK293 cells with reduced endogenous DKK3b. Basal
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Fig 4. Characterization of DKK3b loss of function in MEFs. (A) QPCR analysis of shRNA knockdown of
Dkk3 and û-catenin in MEFs. Data reported as means ± se, n = 3. (B) Basal TOPflash activity in shRNA KD
MEFs. Data reported as the means ± se, n = 6. (C) Quantification of unattached, viable cells after 72 h in
Dkk3/Dkk3b KD MEFs. Viability determined by Trypan blue exclusion; data reported as means ± se, n = 3. (D)
Representative photomicrographs of GFP-expressing, shRNA KD MEFs. TAT-DKK3b (1 μg/ml) was added to
the growth medium as indicated. GFP positive KD cells in 10 random fields were counted for each KD
condition and the data reported as the means ± SD. (E) Quantitative analysis of the attached cells in part D. A
total of 100 cells counted and the data expressed as cells/mm2. Data represent the means ± se, n = 6 wells for
each condition. Taken together, these data show that our promoter-trap knock-in gene-editing strategy: i)
selectively eliminated expression of the intracellular DKK3b; and ii) preserved expression of the secreted
DKK3. Loss of DKK3b in MEFs led to elevated nuclear û-catenin levels, increased û-catenin signaling, and
defective cell attachment to the substratum.
cell proliferation was unaffected by ectopic DKK3b produced either by transient transfection
and by addition of the TAT-DKK3b (Fig 6A and 6B). On the other hand, Wnt-stimulated cell
proliferation was progressively slowed, but not arrested in cells treated with DKK3 by either
transient transfection or by TAT-Dkk3b (Fig 6B). The more robust decrease in proliferation
observed with TAT-DKK3b treatment is likely due to the more uniform delivery of the tumor
suppressor to the cell monolayer. Concentrations of TAT-DKK3b 2.5 μg/ml completely
silenced Wnt-stimulated cell proliferation without altering basal cell proliferation (Fig 6B,
compare basal and Wnt stimulated proliferation at 2.5 μg/ml TAT-DKK3b).
Primary and downstream promoter-luciferase reporter assays determined the effects of
DKK3b on û-catenin-driven gene expression. HEK293 cells were co-transfected with Wnt1
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Fig 5. DKK3b regulation of cell proliferation. (A) Comparison of the effects of DKK3b and DKK3 on PC3
cell proliferation. Representative photomicrographs of immune-reactive, Dox-induced DKK3b and DKK3
expression in PC3 cells. Cell proliferation over 5 days (open symbols, no Dox; solid symbols, Dox; each
symbol a separate experiment; time points determined in triplicate for each experiment). (B) DKK3b arrests
cell proliferation at the G0/G1 phase of the cell cycle (Error bars represent the SE of three independent
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Fig 6. DKK3b effects on Wnt1-stimulated û-catenin signaling. (A) Representative photomicrographs of
the cellular distribution of transiently transfected DKK3b and TAT-DKK3b in HEK293 cells. DKK3b identified
with anti-Flag IgG and anti-DKK3 IgG, respectively. (B) DKK3b blocks Wnt1-stimulated cell proliferation
without altering basal cell proliferation. Data reported as means ± se of 4 independent experiments; n = 3 in
individual experiments. Open barÐday 1; shared barsÐday 3. (C) TAT-DKK3b antagonizes Wnt1-stimulated
TOPflash activity and secondary û-catenin dependent gene expression. Data reported as means ± se of 3
independent experiments; triplicate determinations done in individual experiments.
and promoter-driven firefly luciferase constructs paired with a control CMV-driven renilla
luciferase cDNA, and then treated with TAT-DKK3b for 24 h. Wnt1 stimulated cells showed a
65-fold increase in TOPflash activity and TAT-DKK3b completely arrested expression of this
canonical û-catenin reporter (Fig 6C). DKK3b also modulated downstream û-catenin
regulated pathways that reduce cell adhesion (ECad promoter [
]) and promote cell cycle
progression (E2F promoter [
]). Wnt1 silenced E-Cad promoter activity by 90%, but the presence of
TAT-DKK3b restored promoter activity to basal levels (Fig 6C). Similarly, Wnt1 increased
E2F-promoter activity 6-fold, but the presence of TAT-DKK3B maintained E2F-promoter
activity at baseline levels (Fig 6C). Taken together, these data show that DKK3b modulates
multiple aspects of û-catenin signaling.
DKK3b blocks nuclear translocation of û-catenin
Yeast two hybrid screens showed that DKK3 interacted with the E3 ubiquitin protein ligase,
ûTrCP, and that this complex captured cytoplasmic dephosphorylated û-catenin [
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the source of the essential intracellular effector produced by the Dkk3 gene was not identified
]. DKK3b provides just such an intracellular effector.
Co-IP studies were done with lysates of HEK293 cells constitutively expressing
epitopetagged DKK3b, û-TrCP and the constitutively active S33Y mutant of û-catenin that evades the
destruction complex. When all three proteins were present, immune precipitates of
Flag-S33Yû-catenin also contained both û-TrCP and DKK3b, while control IgG precipitates
failed to capture any epitope tagged targets (Fig 7A). Similarly, immune precipitates of
myc-ûTrCP contained both S33Yû-catenin and DKK3b; immune precipitates of HA-DKK3b
contained both S33Yû-catenin, and û-TrCP (Fig 7A). Co-IP studies of cell lysates expressing only
two of the three binding partners (Myc-û-TrCP and HA-DKK3b) or (FLAG-S33Yû-catenin
and HA-DKK3b) failed to show any interaction between these epitope-tagged binding
partners (Fig 7B). These data suggest that DKK3b captures unphosphorylated û-catenin in a
complex with û-TrCP and that all three partners are required to assemble this complex.
The role of û-TrCP in the DKK3b:û-TrCP:û-catenin complexes on nuclear trafficking and
gene expression was examined in ß-TrCP KD HeLa cells. Immunoblot analysis confirmed
shRNA dependent loss of the ß-TrCP transcript in KD cells (Fig 7C). To maximize nuclear
localization of û-catenin, control and ß-TrCP KD cells were treated with LiCl, a chemical
mimic of Wnt that stabilizes cytosolic û-catenin by inhibiting its phosphorylation by GSK-3 in
the destruction complex [
]. The effects of the DKK3b:û-TrCP:û-catenin complex on
û-catenin-driven gene expression in ß-TrCP KD HeLa cells was then evaluated using the TOPflash
assay. In both resting and LiCl-stimulated control and non-silencing KD cells, addition of
TAT-DKK3b silenced TOPflash activity (Fig 7D). In ß-TrCP KD cells, TAT-DKK3b had no
effect on TOPflash activity, whereas rescue of the ß-TrCP KD by transfection with mouse
ûTrCP cDNA restored the ability of TAT-DKK3b to arrest TOPflash activity in both resting
and LiCl-stimulated cells. These data show that the DKK3b:û-TrCP:û-catenin complex alters
the ability of the û-catenin to enter the cell nucleus and blocks û-catenin-driven gene
The effects of DKK3b on the dynamics û-catenin nuclear trafficking was determined in
LiCl stimulated HeLa cells. HeLa cells lack native Dkk3/Dkk3b expression and show
accelerated û-catenin-driven cell proliferation [
]. As expected, HeLa cell û-catenin was distributed
throughout the cell interior with marginal localization at the cell periphery (Fig 8A). In the
absence of DKK3b, LiCl led to the rapid accumulation of û-catenin in the nucleus reaching
maximal levels after 60 min in >70% of the treated cells, and this remained constant for 18 h
when LiCl was present (Fig 8A and 8B). Addition of TAT-DKK3b along with LiCl completely
blocked the accumulation of nuclear û-catenin for up to 18 h.
The time dependent efflux of nuclear û-catenin due to TAT-DKK3b was determined in
HeLa cells stimulated with LiCl for 18 hrs. Addition of TAT-DKK3b to these maximally
stimulated cells resulted in the rapid loss of nuclear û-catenin, beginning within 30 min and
reaching maximal suppression by 60 min (Fig 8C). TAT-DKK3b-suppressed nuclear û-catenin
below levels in untreated HeLa cells for at least 3 h. Total HeLa cell û-catenin levels were
unaffected by TAT-DKK3b (Fig 8D) indicating that the loss of û-catenin from the nucleus in
TAT-DKK3b treated cells was due to cellular redistribution rather than enhanced û-catenin
degradation. Anti-DKK3b-IgG-affinity beads were used to capture DKK3b associated native
proteins in the LiCl-stimulated HeLa cell lysates (Fig 8E). The loss of nuclear û-catenin in
LiCl-stimulated cells was accompanied by the time-dependent accumulation of both û-catenin
and û-TrCP in a complex with the TAT-DKK3b (Fig 8E). Total cellular levels of both
û-catenin and û-TrCP were unaltered during the 3 h TAT-DKK3b treatment period, while
intracellular DKK3b showed a time-dependent accumulation in the complex that paralleled the loss of
û-catenin from the cell nucleus (Fig 8E). Thus, the DKK3b:û-TrCP:û-catenin inhibitory
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Fig 7. Characterization of the DKK3b:û-TrCP:û-catenin complex and its effects of û-catenin nuclear translocation/
signaling. (A) Co-IP of DKK3b, û-TrCP and û-S33Ycatenin from HEK293 cell lysates. Epitope tagged targets were
expressed by transient transfection in HEK293 cells, immune precipitates collected by Protein A/G Sepharose, and
coprecipitating partners were analyzed by immunoblot with epitope specific antibodies. (B) Co-IP of HEK293 cell lysates
lacking one binding partner. (C) shRNA knockdown of û-TrCP in HeLa cells. Immunoblots done with anti-TrCP IgG. (D)
Effects of û-TrCP KD and û-TrCP rescue on TAT-DKK3b dependent inhibition of TOPflash activity in HeLa cells.
Unaltered, non-silencing control, û-TrCP KD cells, and rescued û-TrCP KD cells expressing a mouse û-TrCP rescue
plasmid were stimulated with ±LiCl for 16h in the absence or presence of TAT-DKK3b (5 μg/ml). TOPflash activity reported
as fold change from resting HeLa cells. Data are reported as the means ± se (n = 4); each experiment was repeated 3
complex is formed rapidly, interrupts the dynamics of nuclear import/export, and defines the
molecular basis for the silencing of û-catenin signaling by DKK3b.
Since DKK3b silenced both TOPflash activity and captured the native transfactor in an
inhibitory complex with DKK3b:û-TrCP, we determined the effects of TAT-DKK3b on native gene
expression in resting and LiCl-stimulated HeLa cells. Like the TOPflash assay, addition of
TAT-DKK3b to unstimulated HeLa cells led to a 40±60% decrease in both native CyclinD1 and
c-Myc transcripts after 16 h (S3A Fig). Similarly, in both resting and LiCl-stimulated cells, the
expression of 5 representative û-catenin dependent genes Cdh2, Axin2, Cox2, Wfdc2 and Fosl1
all showed DKK3b dependent silencing (S3B Fig), while expression of the û-catenin
independent Gapdh used for normalizaiton, and alpha tubulin (Tuba) transcripts were unaffected. These
data show that both reporter and intrinsic gene expression are modulated by ability of DKK3b
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Fig 8. Effects of TAT-DKK3b on the dynamics of û-catenin nuclear translocation. (A) Representative
photomicrographs of the distribution of û-catenin in control (unstimulated) and LiCl-stimulated HeLa cells ± TAT-DKK3b
(arrowsÐcell nucleus). (B) Time course of LiCl-induced nuclear translocation of û-catenin in HeLa ± TAT-DKK3b (5 μg/ml).
At least 200 cells were counted in 20 random fields from 3 individual slides; data reported as means ± SD. (C) Time course of
the effects of TAT-DKK3b on steady-state nuclear û-catenin in LiCl-stimulated HeLa cells. Nuclear û-catenin positive cells
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were scored as in B, and the data reported as means ± SD of 3 independent experiments. (D) Immunoblot of the effects of
TAT-DKK3b on û-catenin levels in HeLa cell lysates. Data reported as means ± se, n = 3. (E) Time dependent assembly of
the TAT-DKK3b:û-TrCP:û-catenin complex in LiCl-stimulated HeLa cells. Cell lysates were incubated with anti-DKK3b-IgG
or NRS-conjugated DynaBeads, and co-precipitating proteins determined by immunoblot with anti-target antibodies.
to control û-catenin translocation to the cell nucleus, and that this action depends on the the
ability of DKK3b to capture the native transactivator in an extranuclear complex with û-TrCP.
DKK3 is the enigmatic member of an ancient family of secreted glycoproteins that regulate the
Wnt/û-catenin pathway by interrupting the assembly of a functional Wnt liganded receptor
]. It is the only unambiguous tumor suppressor in the family, and a diverse literature
links DKK3 and tumor suppression to the û-catenin pathway . Unfortunately, the inability
of DKK3 to block Wnt receptor assembly due to steric hindrance [
] poses a significant
challenge to our understanding of its tumor suppressor function. Yeast two-hybrid screens
 showed that DKK3 formed a complex with û-TrCP, and dephosphorylated û-catenin that
prevented transfactor nuclear translocation [
], but Lee and co-workers did not identify the
authentic intracellular DKK3 isoform responsible for this biology.
The recognition that the Dkk3 gene encodes a second gene product, DKK3bÐa vital
intracellular protein that regulates û-catenin traffickingÐprovides the missing component that
connects the Dkk3 gene to its regulation of the û-catenin signaling pathway. DKK3b acts on
the û-catenin signaling pathway independent of the Wnt modulated destruction complex and
modulates a diverse array of cellular functions, such as cell proliferation, cell attachment,
embryogenesis and gene expression. Positioned downstream of the Wnt regulated degradation
complex, DKK3b modulates û-catenin trafficking to the nucleus. In astrocytes, DKK3b rapidly
shuttles between the perinuclear space and the plasma membrane using myosin motors and
actin fibers [
], suggesting that it may carry û-catenin back the cell periphery for reuse in
the adherens complex remodeling. The ability of DKK3b to repair the attachment defect
observed in DKK3b-null MEFs suggests that DKK3b plays a key role in the delivery of
û-catenin to its plasma membrane reservoir.
The Dkk3 gene joins a growing list of mammalian genes that use multiple alternate
promoters to achieve functional diversity [
]. Our identification of a second TSS element in the
Dkk3 gene and the demonstration that it generates a second transcript encoding a vital
intracellular isoform was unexpected. Using targeted gene editing to abolish Dkk3b expression,
while preserving expression of its sister (Dkk3), we found that DKK3b was essential for early
embryonic development at or near implantation, dramatically different from the Dkk3tm1Cni
mutant mouse where secreted Dkk3 expression was inactivated . Despite the presence of
the entire Wnt/û-catenin pathway from oocyte to the late blastocyst stage [
canonical Wnt signaling is not observed in pre-implantation blastocysts , and is first
observed post-implantation at E6.5 [
]. Using a Wnt reporter mouse expressing a functional
mutant of û-catenin that evades the destruction complex, Kemler et al [
] found the stabilized
û-catenin in the cytoplasm of pre-implantation embryos, but that it did not traffic to the
nucleus and no Wnt reporter expression was observed. They suggested that cellular
mechanism(s) other than the canonical destruction complex [
] were responsible for keeping the
stabilized û-catenin out of the cell nucleus before implantation. Since DKK3b is an important
gatekeeper of û-catenin nuclear translocation, its loss in the zygote is likely to unleash
û-catenin signaling that has detrimental consequences on the developing embryo both before
implantation and at this critical developmental event.
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Fig 9. Schematic diagram of the novel regulatory role of DKK3b in the Wnt/û-catenin signaling
pathway. DSH, Disheveled; GSK-3, Glycogen synthase kinase 3 beta; CK1, Casein kinase 1; PP2A, Protein
Phosphatase 2A; APC, Adenomatous Polyposis Coli; û-TrCP, û-Transducin Repeat-Containing Protein; Ub,
DKK3b-deficient MEFs showed both elevated û-catenin signaling and cell attachment
defect(s); two events likely to interrupt orderly development of the embryo. These disruptions
in the signaling pathway were rescued by replacement with ectopic DKK3b or by simultaneous
knockdown of û-catenin. These data illustrate that the loss of DKK3b directly leads to aberrant
û-catenin signaling and disrupts cell-cell and cell-substrate interactions.
Unlike its ubiquitous expression in somatic cells, silencing of the Dkk3 gene is common in
cancer and ectopic over-expression of DKK3 arrests tumor cell growth [16±19]. Analysis of
intracellular product of the Dkk3 gene, revealed that DKK3b arrests Wnt stimulated cell
proliferation and selectively silences û-catenin dependent gene expression in both immortal and
cancer cells. The ability a purified cell-penetrating DKK3b protein to fully restore control of
ûcatenin signaling by partnering with û-TrCP to capture the transfactor in an extra nuclear
complex offers a promising new therapeutic target for û-catenin driven hyper-proliferative
disease(s) like cancer.
An essential partner in the molecular mechanism of DKK3b action is û-TrCP, an
Fbox protein with WD40 repeats that captures a broad range of protein targets through a
consensus dephosphorylated 6 amino acid long degron domain in the target protein(s) that is
located 10 to 20 residues downstream of the lysine used for ubiquitin conjugation [
DKK3b captured dephosphorylated û-catenin in a complex with û-TrCP, prolonged the
biological half-life of the transfactor, and prevented its translocation to the nucleus (Fig 9). Direct
analysis of the dynamics of û-catenin nuclear entry and exit showed that the tripartite complex
21 / 27
trapped the transfactor outside the nucleus providing a clear molecular mechanism for the
DKK3b-dependent regulation of this pathway. Since the N-terminal localized degron of
ûcatenin docks with û-TrCP, the ability of DKK3b stabilize transient interaction(s) between the
dephos-degron of û-catenin and û-TrCP during ªkiss-and-runº interaction(s) [
that other û-TrCP ligands that similarly engage this E3 ligase are potential regulatory targets.
These include members of most of the kinase signaling cascades that impact cell growth,
motility, and apoptosis [71±74]. Further studies are required to determine if DKK3b captures other
û-TrCP interacting proteins and impacts their signaling pathways.
DKK3b is a novel and essential component of the Wnt/û-catenin signaling pathway that
plays a key role in both development and cancer. It serves as a gatekeeper for û-catenin nuclear
entry, directly modulates this pro-proliferative signaling molecule, and provides an important
new point of control that impacts the regulatory pathways responsible for differentiation,
lineage specification, pluripotency and oncogenesis.
S1 Fig. Exon specific qPCR analysis of Dkk3 transcripts in mouse astrocytes. (A) The
position of the PCR primer pairs used for amplification of exon 2 and exon 3 shown on the Dkk3
cds. (B) Validation of the Dkk3 exon 2 and exon 3 primer sets using increasing concentrations
of 1st strand cDNA primed total RNA isolated from two independent mouse astrocyte
preparations. Each data point determined in triplicate. (C) Dkk3 mRNA levels were normalized to
GAPDH mRNA. Data shown as (mean ± SE) from 3 independent experiments.
S2 Fig. 5'RACE analysis of Cfp mRNA from the Dkk3bCFP mouse. (A) Map of the insertion
of the CFP promoter trap in gene-edited intron 2 of the Dkk3 gene. TSS2 is positioned
upstream of the forward LoxP site (black box) of the gene and the downstream LoxP site (in
black) is positions 35 nt upstream of exon 3. Position of the CFP234 5'RACE primer indicated
by arrow. (B) Sequence of the 5'UTR of the Cfp mRNA captured by 5'RACE highlighted in
S3 Fig. Effects of TAT-DKK3b on basal and LiCl-stimulated gene expression in HeLa cells.
(A) Basal CyclinD1 and Myc expression in HeLa cells ±TAT-DKK3b for 16 h. (B) Native
ûcatenin dependent gene expression in HeLa cells. Cells were stimulated with ±LiCl in the
absence or presence of TAT-DKK3b for 16 h. QPCR data are reported as % of unstimulated
controls for each target transcript and expressed as means ± se, n = 9. Gene products probed:
Cdh2, N-cadherin; Axin2, Axin2; Cox2, cyclooxygenase-2; Wfdc2, WAP Four-disulfide Core
Domain 2; Fosl1, FOS Like Antigen 1; Tuba, alpha tubulin.
We thank the UMMS Transgenic Animal Modeling Core for their help with zygote injections
and embryo implantation and the UMMS FACS Core for isolation of gene-edited MEFS.
Conceptualization: Jack L. Leonard, Deborah M. Leonard, Scot A. Wolfe, Karl J. Simin.
Data curation: Jack L. Leonard, Deborah M. Leonard, Jilin Liu, Kate L. Liebmann.
22 / 27
Formal analysis: Jack L. Leonard, Deborah M. Leonard, Scot A. Wolfe, Jaime Rivera, Karl J.
Funding acquisition: Jack L. Leonard.
Investigation: Jack L. Leonard, Deborah M. Leonard, Jilin Liu, Jaime Rivera, Michelle Yang,
Ryan T. Leonard, Jacob P. S. Johnson, Prashant Kumar, Kate L. Liebmann, Amanda A.
Tutto, Zhongming Mou, Karl J. Simin.
Methodology: Jack L. Leonard, Deborah M. Leonard, Scot A. Wolfe, Jilin Liu, Jaime Rivera,
Michelle Yang, Ryan T. Leonard, Jacob P. S. Johnson, Prashant Kumar, Karl J. Simin.
Project administration: Jack L. Leonard.
Resources: Jack L. Leonard, Scot A. Wolfe.
Supervision: Jack L. Leonard.
Validation: Jack L. Leonard, Jilin Liu, Jaime Rivera.
Visualization: Jack L. Leonard.
Writing ± original draft: Jack L. Leonard, Scot A. Wolfe, Jilin Liu, Karl J. Simin.
Writing ± review & editing: Jack L. Leonard, Deborah M. Leonard, Scot A. Wolfe.
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