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Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
http://www.immunotherapyofcancer.org/content/1/1/2
RESEARCH ARTICLE
Open Access
Presence of antigen-specific somatic allelic
mutations and splice variants do not predict for
immunological response to genetic vaccination
Jordan T Becker and Douglas G McNeel*
Abstract
Background: Antigen-specific anti-tumor vaccines have demonstrated clinical efficacy, but immunological and
clinical responses appear to be patient-dependent. We hypothesized that naturally-occurring differences in amino
acid sequence of a host’s target antigen might predict for immunological outcome from genetic vaccination by
presentation of epitopes different from the vaccine.
Methods: Using peripheral blood cells from 33 patients who had been treated with a DNA vaccine encoding
prostatic acid phosphatase (PAP), we sequenced the exons encoding PAP and PSA genes from somatic DNA to
identify single nucleotide polymorphisms. In addition, mRNA was collected to detect alternative splice variants
of PAP.
Results: We detected four synonymous coding mutations of PAP among 33 patients; non-synonymous coding
mutations were not identified. Alternative splice variants of PAP were detected in 22/27 patients tested. The
presence of detectable splice variants was not predictive of immunological outcome from vaccination. Immune
responses to peptides encoded by these splice variants were common (16/27) prior to immunization, but not
associated with immune responses elicited with vaccination.
Conclusions: These results suggest that antigen-specific immune responses detectable after treatment with this
genetic vaccine are specific for the host-encoded antigen and not due to epitope differences between the vaccine
and a particular individual’s somatic coding sequence.
Keywords: PAP, DNA vaccines, Alternative splice variants, Allelic variants
Background
Immunotherapies, and antigen-specific vaccines in particular, are of great interest as a means of providing a
tumor-specific therapy with ideally minimal toxicity. The
recent successes with the 2010 FDA approval of
Provenge™ and ipilimumab as treatments for metastatic
prostate cancer and melanoma to prolong survival
underscore the potential of these types of novel therapies [1,2]. In addition, in 2010 the USDA approved the
canine melanoma vaccine, Oncept™, a DNA vaccine encoding human tyrosinase, on the basis of clinical trials
demonstrating improved overall survival of dogs with
melanoma treated with this vaccine [3]. A number of
* Correspondence: [email protected]
Department of Medicine, University of Wisconsin Carbone Cancer Center,
1111 Highland Avenue, Madison, WI 53705, USA
cancer immunotherapeutic vaccines for other malignancies have progressed to Phase II and Phase III clinical trials on the basis of demonstrable clinical benefit [4]. For
example, data from a large Phase II trial of a viral vaccine
encoding prostate-specific antigen, PROSTVAC™, suggested an increase in overall survival of patients with
metastatic prostate cancer [5]. A similar genetic vaccine
targeting MUC1 (TG4010) has been shown to enhance
the effects of chemotherapy in a Phase IIb clinical trial of
patients with advanced non-small cell lung carcinoma
(NSCLC) and this vaccine is now in a Phase IIb/III clinical
trial evaluating first-line safety and clinical efficacy in
prolonging survival [6]. In trials using these antigenspecific vaccines investigators have sought to identify
antigen-specific immune responses as possible biomarkers
for those individuals likely to benefit clinically from
© 2013 Becker and McNeel; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the
Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
http://www.immunotherapyofcancer.org/content/1/1/2
vaccination. However, it has been observed that immunological responses are present in some patients and not in
others, and that immunological response is not always associated with clinical response. Accordingly, some investigators examining cancer immunotherapies in preclinical
and early Phase I and II clinical trials have chosen to
utilize strategies meant to boost the frequency of immunological responders and/or broaden the durability
and quality of the immune responses elicited. Current
strategies under investigation include alternative means of
vaccine delivery, use of adjuvants and/or combination
therapies, use of multiple antigens and/or multiple vaccine
vectors, and taking advantage of xenoantigen crossreactivity [7-12].
Studies from our group and others highlight that DNA
vaccines offer an off-the-shelf, inexpensive, and mutable
therapeutic option with very minimal toxicity and broadly
augmentable clinical applications as far as schedule and
dosing are concerned [7]. Our work with a DNA vaccine
targeting prostatic acid phosphatase (PAP) has shown
clinical safety and immunological efficacy, eliciting durable
PAP-specific T-cell responses capable of amplification by
subsequent booster immunizations [13,14]. Other antigens
currently being targeted by genetic vaccines in human
clinical trials include: carcinoma-embryonic antigen
(CEA), gp100, MAGE-A3, MUC1, NY-ESO-1, prostatespecific antigen (PSA), and prostate-specific membrane
antigen (PSMA) [6,11,15-19].
Antigens encoded by genetic vaccines generally consist
of a native DNA sequence based on readily available
data from genomic and protein databases. Accordingly,
xenogeneic vaccination utilizes highly homologous antigens specific to other species to hopefully elicit immune
responses that cross-react with areas of similar or conserved epitopes. Xenogeneic cross-reactivity has specifically been researched and cited as an effective means of
overcoming self-tolerance to tumor-associated antigens
(TAAs) [12]. Indeed, the USDA approval of Oncept™
(Merial Ltd, Duluth, GA, USA) helped to highlight the
immunological and clinical success of xenogeneic vaccination, specifically the treatment of canine melanoma
with a DNA vaccine encoding human tyrosinase [3].
Xenogeneic vaccination, specifically DNA vaccines using
prime-boost strategies targeting mouse and human
PSMA, have been under investigation for prostate cancer [12]. Recent work from our laboratory has indicated
that Lewis rats immunized with DNA vaccine encoding
human PAP generate responses to the highly homologous human antigen; in fact, these responses recognize a
single epitope that differs from the rat PAP sequence by
only two amino acids. However, in this particular system
there is no evidence of cross-reactivity to the corresponding rat epitope [20]. Conversely, Copenhagen rats
immunized with vaccinia vector encoding human PAP
Page 2 of 13
generate cytotoxic T lymphocyte (CTL) responses and
subsequently experience prostatitis, indicative of an immune response against rat PAP [21]. These results suggest that xenoantigens may or may not elicit productive
anti-tumor immune responses, and the effects might be
dependent upon the MHC type of the host. Analogously,
we speculated that if a DNA vaccine encoding a standard antigen sequence was administered to patients who
actually expressed a variation of that antigen, the
vaccine-encoded-antigen (or some epitopes encoded)
might be recognized as “foreign” in those patients. Thus,
we reasoned that single nucleotide polymorphisms
(SNPs) in the somatic PAP genes of patients might represent very highly homologous antigens and might be an
avenue for enhanced immune response following
antigen-specific vaccination, or alternatively might explain why immune responses occur, detectable to the
homologous-but-foreign antigen, that are not associated
with clinical response.
Using available online database resources we observed
that others have previously detected SNPs among individuals’ genes encoding PAP (Ensembl Online Database).
One previously detected SNP found among these data occurs in p299-307, a previously defined HLA-A2-restricted
epitope of human PAP protein [22,23]. Additionally, a
number of alternative splice variant messenger RNA transcripts exist for PAP, notably three protein-coding alternative splice variant transcripts. Allelic variants in the
somatic gene encoding PAP, as well as preferentiallyexpressed alternative splice variants of PAP, may represent
very highly homologous antigens distinct from the
vaccine-encoded antigen. In the current report we sought
to determine the frequency of PAP target gene SNPs and
the frequency of alternative splice variants of PAP in our
patient population, as well as their associations with immune response following vaccination.
Results
Amino acid coding mutations have been previously
detected among common anti-tumor genetic vaccine
antigens
Our laboratory and others have investigated anti-tumor
genetic vaccines targeting a variety of protein antigens in
clinical trials of breast cancer, gastrointestinal malignancy, melanoma, non-small cell lung cancer, ovarian
cancer, and prostate cancer. Allelic variants have been
detected for many of the common anti-tumor genetic
vaccine antigens. Prepared using online resources,
Table 1 summarizes the size and chromosomal location
of genes encoding several common target antigens and
highlights the frequency of previously identified SNPs in
these genes. Notably, SNPs have been previously
detected in the gene encoding PAP, the target of FDAapproved sipuleucel-T (Provenge™, Dendreon Corp.,
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Page 3 of 13
Table 1 Human genes encoding common target antigens of genetic vaccines show previously detected allelic
variations
Target antigen
Gene ID
AR
CEA
AR-001 CEACAM5-001
gp100
PMEL-001
MAGE-A3
NY-ESO-1
PAP
PSA
PSMA
MAGEA3-001 CTAG1B-001 ACPP-001 KLK3-201 FOLH1-001
TYR
TYR-001
Location
Xq12
19q13.1-13.2
12q13-q14
Xq28
Xq28
3q21-q23
19q13.41
11p11.2
11q14-q21
Synonymous Coding Mutations
26
28
22
16
0
13
20
19
24
Non-Synonymous Coding
Mutations
71
61
46
43
1
22
39
38
95
Stop Gain/Loss
6
1
2
0
0
3
0
0
9
Frameshift
1
1
0
0
0
0
2
2
13
Coding Unknown
337
0
0
0
0
0
0
1
207
Total
441
91
70
59
1
38
61
60
348
cDNA Length (bp)
10065
2907
2757
1724
998
3125
1464
2635
2466
Protein Length (aa)
920
702
661
314
168
386
261
750
529
Mutation Quotient
0.085
0.090
0.073
0.137
0.006
0.065
0.157
0.053
0.221
Eight genes encoding genetic vaccine target antigens under investigation in human clinical trials, and one gene encoding a prostate cancer target antigen of
interest (AR), are listed in this table by antigen name as well as Gene ID taken from the USEast Ensemble online database. The NCBI-Gene and USEast Ensemble
online databases provided information regarding chromosomal location of antigen gene, cDNA length (bp), and protein length (aa) as well as total number of
allelic variations previously detected by others. Allelic variations are categorized into synonymous, non-synonymous, stop gain/loss, frameshift, or unknown coding
mutations accordingly. Mutation quotient is defined as the sum of non-synonymous coding mutations, stop gain/loss, and frameshift mutations (mutations that
could affect immunologically presented epitopes) divided by protein length (aa). Coding mutation online queries were performed April 16, 2012.
Seattle, WA, USA) as well as the target of a DNA vaccine currently being investigated in a Phase II clinical
trial [1]. We included a “mutation quotient” in Table 1,
defined as the sum of all exonic non-synonymous, stop
loss/gain, and frameshift coding mutations, mutations
that could specifically affect MHC-presented epitopes,
for each gene divided by the amino acid (aa) length of
the protein product. We observed that while some common vaccine target antigens are highly conserved (e.g.
NY-ESO-1), others are not. For instance, 41 amino acid
coding mutations that could affect presented epitopes
have been detected in the gene encoding PSA (261 aa
protein), whereas in the gene encoding PAP (386 aa)
only 25 amino acid coding mutations have been
detected. We focused these experiments on PAP as it is
the target antigen of the FDA-approved sipuleucel-T and
given that we have previously detected PAP-specific immune responses in a subset of patients receiving a genetic vaccine, pTVG-HP, encoding this antigen.
Allelic variations in patient PAP gene are detectable but
non-synonymous coding mutations are not associated
with differences in PAP-specific immune responses
Our previously published reports indicate that multiple
patients receiving anti-tumor vaccination against the
self-antigen PAP showed evidence of antigen-specific
immune responses detectable either post-vaccination or
developing up to one year following immunization
[13,14]. However, we failed to detect PAP-specific immune responses in some patients and additionally, in an
on-going Phase Ib/II clinical trial using the same vaccine, we have observed similar differences in immune
response development (unpublished data). We hypothesized that non-synonymous allelic variations in patient
PAP gene could relegate vaccine-encoded PAP protein
as essentially foreign, thereby increasing the immunogenicity of the DNA vaccine. Consequently, we sought
to examine whether SNPs of the gene encoding PAP
could be detected in the somatic DNA of patients receiving antigen-specific genetic vaccination targeting
PAP. We then wished to determine whether patient immune response following antigen-specific vaccination
was associated with detectable allelic variations in the
target antigen, PAP.
Using primers indicated in Additional file 1: Table S1,
we sequenced genes encoding PAP from genomic DNA
extracted from PBMC from a total of 33 patients.
Among the ten exons of PAP, we detected four SNPs or
allelic variants (Figure 1A). Six patients expressed a T>G
transversion in the first codon of PAP exon 2 (PAPc.122T>G, 6/33, 18.18%). Eleven patients expressed a
C→T transition in the 23rd codon of PAP exon 8 (PAPc.849C>T, 11/33, 33.33%). Fifteen patients expressed a
T→C transition in the ninth codon of PAP exon 10
(PAP-c.993T>C, 15/33, 45.45%). Seventeen patients
expressed an A→G transition in the 60th codon of PAP
exon 10 (PAP-1146A>G, 17/33, 52.52%). As demonstrated in Table 2, we observed that the expression of
PAP-c.122T>G differed significantly between immune
responders and non-responders (p=0.0015, Fisher’s exact
test). However, all of the PAP SNPs detected in our patients were synonymous coding mutations, producing no
alterations in the amino acid sequence of the PAP protein. Thus, contrary to our hypothesis, patients with
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Figure 1 Allelic variants in patient PAP and PSA genes are detectable. Sanger sequencing was conducted to identify allelic variants in
patients’ PAP gene (A) and PSA gene (B). Allelic variants are highlighted to indicate either synonymous (gray) or non-synonymous (black) coding
mutations. Coding mutations are designated with transversions K (keto) and M (amino), as well as transitions R (purine), and Y (pyrimidine) IUPAC
nucleotide ambiguity codes.
evidence of PAP-specific immune responses did not encode PAP protein different in amino acid sequence from
the immunization vector-encoded PAP and it was therefore unlikely that immune responses detected following
vaccination were due to responses to epitopes differing
between the host and immunization vector.
Allelic variations in patient PSA gene are detectable and
encode changes in amino acid sequence
Among these same 33 individual patient samples, we
also sequenced patients’ genes encoding PSA as it is not
only the target antigen of other genetic vaccines,
PROSTVAC and a plasmid DNA vaccine, but is also the
primary serum marker protein used in the diagnosis of
prostate cancer and the most widely used cancer biomarker [24,25]. Among five exons of PSA, we detected
seven SNPs (Figure 1B). Two patients expressed a T→G
transversion in the first codon of PSA exon 2 (PSAc.48T>G, 2/33, 6.06%). One patient expressed an A→C
transversion in the third codon of PSA exon 2 (PSAc.54A>C, 1/33, 3.03%). One patient expressed a C→T
transition in the 13th codon of PSA exon 2 (PSAc.84C>T, 1/33, 3.03%). Seven patients expressed a C→T
transition in the 11th codon of PSA exon 3 (PSAc.237C>T, 7/33, 21.21%). These four SNPs were synonymous coding mutations and as such did not encode
for a change in the amino acid sequence of PSA protein.
However, we also detected three SNPs of a nonsynonymous nature. Two patients expressed a G→A
transition in the 34th codon of PSA exon 3 resulting in
a D102N amino acid change (PSA-c.304G>A, 2/33,
6.1%). Four patients expressed a C→A transversion in
the 64th codon of PSA exon 3 resulting in an L132I
amino acid change (PSA-394C>A, 4/33, 12.1%). Two patients expressed a T→C transition in the 15th codon of
PSA exon 4 resulting in an I179T amino acid change
(PSA-c.536T>C, 2/33, 6.1%). Thus, albeit in a small patient population, amino acid divergent allelic variants of
PSA, a smaller protein, were more common than those
of our target antigen, PAP.
Transcript variants of PAP are detectable by RTPCR from
patient PBMC samples
Although we found that all patients receiving antigenspecific vaccination shared complete protein homology
with the immunizing vector encoding PAP, messenger
RNA transcripts exist for the native protein as well as
eight other alternative splice variants. In total, there are
four known protein-coding transcripts of PAP including
ACPP-001 (native PAP), ACPP-002, ACPP-003, and
ACPP-004 [26]. We hypothesized that expression of PAP
alternative splice variants could present an additional set
of antigenic epitopes not encoded by vaccine and, if
expressed preferentially, may render immune responses
to vaccine irrelevant and inform why immune response
is not necessarily equivalent to clinical response following antigen-specific vaccination. We consequently
sought to determine whether we could detect native
and/or splice variant transcripts of PAP in our patients.
Without an available resource of prostate or tumor
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Table 2 Patients express multiple allelic variations of PAP and PSA genes
PAP allelic variants
Non-Responders
PSA allelic variants
Patients
122T>G
849C>T
993T>C
1146A>G
1
X
X
X
X
2
X
X
X
X
3
X
4
X
5
X
6
X
48T>G
54A>C
84C>T
237C>T
304G>A
394C>A
536T>C
X
X
7
X
X
X
8
X
X
X
X
9
10
11
12
13
X
X
X
X
X
X
X
X
X
X
X
X
X
20
X
X
21
X
X
14
15
16
17
18
19
X
X
X
X
22
23
Immune Responders
X
X
X
X
24
25
X
26
27
X
X
X
X
X
X
X
28
X
29
X
30
31
X
X
X
X
X
X
X
X
X
X
X
X
32
33
Shown are individual SNPs detected among PAP-specific immune non-responding patients (top, 1–13) and PAP-specific immune responding patients (bottom,
14–33). Detected allelic variants are named for their relative position within each gene such that PAP-c.122T>G is the T→G transversion in the 122 nucleotide
from the cDNA start site. Detection of an allelic variant is indicated by an X. Bold face indicates synonymous coding mutations and bold face italic indicates
non-synonymous coding mutations.
biopsies from these patients, we collected mRNA from
patient PBMC samples collected prior to vaccination
and performed RTPCR. To detect the PAP variants
ACPP-002 and ACPP-004, we designed primers that
would yield a native PAP product as well as, if present,
a variant PAP product of a smaller size (Figure 2A). To
detect ACPP-003, we designed primers that would
yield an amplicon specific to the transmembrane
domain without amplifying native PAP. Figure 2A depicts the eleven pertinent exons of the four known
protein-coding transcripts of PAP, shows the splice
variant specific alterations for each member, and indicates the expected sizes of amplified regions using the
primers designed (listed in Additional file 2: Table S2).
Following RTPCR amplification of mRNA from 27 patients with pre-vaccination PBMC still available, we
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Page 6 of 13
hindered nor enhanced by their presence. As such their
presence does not represent a means of circumventing
immune responses to the native antigen.
Immune responses to regions specific to PAP splice
variants are detectable in patients prior to vaccination
with antigen-specific DNA vaccination
Figure 2 Native and splice variant mRNA transcripts of PAP are
detectable in patients prior to vaccination. Panel A: Shown
schematically are the four protein-coding transcripts of PAP
including exons which are retained or excluded. Primer sets for
ACPP-002 and ACPP-004 were designed to yield a native PAP
product of indicated size as well as, if present, a variant PAP product
of indicated size and as indicated by the gray boxes. Primer set for
ACPP-003 was designed to yield a PAP-TM product of indicated size
specific to the transmembrane domain-coding region of that
transcript. Panel B: A representative agarose gel image of RTPCR
products shows β-actin in lane 1, KLK3 (PSA) in lane 2, ACPP-002
native and variant bands in lane 3, ACPP-003 in lane 4, ACPP-004
native and variant bands in lane 5, no template control in lane 6,
and 50 bp DNA ladder in lane 7.
found that detection of these four protein-coding transcripts was common in non-responding as well as
immune-responding patients (Figure 2B and Table 3).
Direct sequencing of isolated bands confirmed that
RTPCR amplified expected transcripts of native PAP and
splice variants of PAP (data not shown). We detected
PSA transcripts in some prostate cancer PBMC samples
(Table 3) but not in PBMC samples from volunteer
blood donors (n=3, data not shown). Surprisingly, we
did detect native PAP and/or one of the splice variants
in three of three PBMC samples from patients without
prostate cancer (data not shown). These results warrant
further investigation into the transcriptional regulation
and tissue-specificity of native PAP and splice variants;
future studies are planned to expand upon these results.
Nonetheless, the presence of detected alternative splice
variants in patients with and without immune responses
elicited to the native protein suggested that immune
response to antigen-specific vaccination is neither
We have observed PAP-specific immune responses in patients prior to vaccination that were augmented following
antigen-specific vaccination [14]. In addition, we have previously reported that PAP-specific T-cell proliferative immune responses are detectable in ~11% of patients with
prostate cancer irrespective of immunization [27]. In the
current study, because patients expressed detectable transcripts of native and splice variant PAP, and in particular
because expression of the splice variants was quite common among patients tested, we questioned whether patients who possessed detectable native PAP and/or PAP
splice variant transcripts might exhibit immune responses
to peptide epitopes specific to PAP splice variants. As such,
to identify immune responses specific for the native or
splice variants of PAP, we designed 15-mer peptide pools
specific to the splice junctions of each alternative splice
variant PAP protein (Figure 3A and B) and used a peptide
pool comprised of 38 individual 15-mer overlapping peptides spanning the full length of the native PAP protein to
identify immune responses to the native protein (ACPP001) [28]. Among 27 patients tested for IFN-γ-secreting
immune responses to alternative splice junction peptide
pools from samples collected prior to clinical vaccination,
we found evidence of immune response to the native PAP
pool (PAP1-386) in 2 patients, similar to our previous report
[27]. Responses to most splice variants were at a similar
frequency, however responses to a portion of the transmembrane ACPP-003 (s3p2 pool) were detected at a high
frequency, in 15 (56%) patients (Table 4). There was no difference in the frequency of this baseline response between
immune responders and non-responders (p=1.0, Fisher’s
exact test). Overall these results suggest that alternative
splice variants of PAP are detectable in patients, some patients possess baseline immune responses to regions specific to those variants as well as to the native PAP, and
immune responses to the transmembrane transcript variant of PAP were particularly common in these patients
with prostate cancer. While these results suggest that the
transmembrane variant of PAP might be particularly immunogenic, the presence of immune responses specific to
the transmembrane transcript did not preclude the development of immune responses to the native PAP protein
following immunization.
Discussion
At the outset of this investigation we questioned whether
differences in immune response following antigen-specific
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Table 3 mRNA transcripts of native and splice variants of PAP are detectable in pre-vaccination patient PBMC
PAP mRNA transcripts
ACPP-002
Control mRNA transcripts
Patients
ACPP-001
ACPP-003
1
X
2
X
X
X
3
X
X
X
4
X
X
X
β-actin
KLK3-201
X
X
X
X
X
X
X
ACPP-004
X
5
Non-Responders
X
X
X
7
X
X
X
X
8
X
X
X
X
X
X
X
11
X
12
X
X
X
X
X
X
X
X
X
X
X
13
Immune Responders
X
X
6
10
X
X
X
X
14
X
X
15
X
X
16
X
X
17
X
18
X
19
X
X
X
24
X
X
X
25
X
X
X
X
X
X
X
X
X
X
26
X
X
X
X
X
X
X
X
X
X
X
27
X
28
X
X
X
X
29
X
X
31
X
X
32
X
33
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Shown are native and alternative splice variant PAP products detected among immune non-responding patients (top, 1–13) and immune responding patients
(bottom, 14–33). Detection of an mRNA transcript is indicated by an X.
vaccination might be due to a phenomenon similar to
xenogeneic cross-reactivity. Specifically, we hypothesized
that patients expressing highly homologous allelic variants
and/or alternative splice variants of PAP might present
different epitopes than those encoded by the vaccine, permitting the vaccine to invoke a cross-reactive response to
homologous epitopes. This seems to not be the case for
these patients and this antigen. However, we believe these
findings are novel and relevant to the tumor immunology
field in that: 1) this is the first examination of the allelic
variation of a somatic gene targeted by genetic vaccination
among patients receiving said vaccine; 2) this is the first
report showing detection of mRNA transcripts of native
PAP and alternative splice variants of PAP from peripheral
blood samples; 3) this is the first evaluation of associations
between immune response to vaccination and the detection of allelic or transcriptional antigen variants; and 4)
this report effectively demonstrates in humans that
antigen-specific immunization can elicit a response to the
host genome-encoded antigen. In addition, our report
demonstrates that IFN-γ-secreting immune responses
specific for alternative splice variants of PAP are common,
suggesting that, in particular, the transmembrane variant
of PAP might be a relevant immunological target antigen
for future investigation.
We detected synonymous coding mutations of PAP in
the somatic DNA of 33 patients that went on to receive
a genetic vaccine encoding an antigen with an amino
acid sequence identical to their own (pTVG-HP). Our
initial interest was that genetic variation in the target
antigen could predict or inform immunological response
to subsequent vaccination. We have previously published
results indicating that some patients developed immune
responses following vaccination with pTVG-HP and
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
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Page 8 of 13
Figure 3 Peptides specific to PAP splice variant proteins designed for the detection of pre-existing immune responses span splice
junctions of variant proteins. Panel A: Shown is an amino acid sequence alignment of the four protein coding alternative splice variants of PAP
with the native PAP protein. Panel B: Shown are the amino acid sequences of five peptide pools spanning the alternative splice variants of PAP,
including three pools for the transmembrane domain of ACPP-003.
others did not, and the present sequencing results suggest that detectable immune responses were likely reactive to the PAP self-antigen in contrast to other vaccines
which take advantage of xenoantigen cross-reactivity to
elicit responses [13,14]. While this is the probable case
for these patients immunized with PAP-targeted vaccines, immunogenicity and frequency of allelic variation
of other vaccine antigens (such as gp100, PSMA, PSA
and tyrosinase) may differ greatly from those known
presently. More to the point, these results suggest that
vaccination with pTVG-HP, or sipuleucel-T which similarly targets PAP, are truly targeting the antigen of interest, rather than a highly homologous or “foreign”
protein. However, it should be noted that we examined
the expression of allelic variation in somatic DNA coding for the target antigen. PAP protein expression can
increase with progression of prostate cancer, being
expressed on AR-negative neuroendocrine cells, and it is
thus possible that due to an evolving karyotype, genetic
mutation of proteins expressed by tumor cells (not detectable in our analysis) could allow for immune evasion
following vaccination [29]. In the present study, patient
tumor samples were not available to evaluate the association between PAP mutations in tumor cells and immune response to PAP-specific vaccination. Moreover,
the trials from which these samples were obtained accrued patients with minimal residual disease, without
radiographic evidence of metastases, hence such samples
were not available. Certainly, future studies examining
differences in immune response to vaccination with respect to possible variations in tumor-encoded antigen
could be informative.
As shown in Table 1, PAP is one of the more highly
conserved vaccine target antigens currently under
investigation. PSA is less conserved, with a greater number of protein-altering mutations previously detected,
despite it being a protein of fewer amino acids. While
we detected non-synonymous coding mutations of PSA
we cannot know the impact this may (or may not) have
on the efficacy of a genetic vaccine encoding PSA in
these patients. As these allelic variants encode for an
amino acid sequence different from the native PSA protein, broader investigation of variants of this antigen is
warranted [30,31]. PROSTVAC™ is a genetic vaccine encoding PSA currently being investigated in Phase III
clinical trials, and with such a large patient population
associations of immunological and/or clinical response
with expression of non-synonymous coding mutations of
PSA might be possible. Serum PSA protein replaced
PAP as the standard clinical biomarker for the detection
and diagnosis of prostate cancer, as well as for staging
and monitoring prostate cancer progression [32,33].
Both of these prostate-specific serum proteins, PAP and
PSA, are measured in the serum of patients with prostate cancer, using immunometric assays specific to each
protein [34]. Immunometric assays allow sufficient sensitivity for the detection of small quantities of secreted
protein as biomarkers. However, this assay utilizes antibodies that recognize specific epitopes of the protein to
be measured. In patients expressing non-synonymous
coding mutations or alternative splice variants within
recognized epitopes which alter antibody binding,
detection and measurement of serum protein could be
compromised.
In the present study, we did not observe differences between immune non-responding and immune responding
vaccine patients in their expression of allelic variants of
PAP or in their expression of alternative splice variants of
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
http://www.immunotherapyofcancer.org/content/1/1/2
Page 9 of 13
Table 4 Immune responses to peptides specific to PAP splice variant proteins are detectable in patients
Library
Patients
hPP
Splice junction peptide pools
s2p1
1
2
X
s3p2
X
X
X
X
X
X
3
s3p3
Control antigens
s3p1
s4p1
rPP-100
X
X
X
X
X
5
X
6
X
7
X
8
X
10
X
X
11
X
X
12
X
X
13
X
14
15
X
X
X
X
16
X
X
X
17
18
X
X
X
X
19
24
Immune responders
PHA
X
4
Non-responders
SSX2-p167
X
X
X
X
X
X
X
X
25
X
X
26
X
X
27
X
X
28
X
X
29
X
X
31
X
X
X
32
X
33
X
X
PBMC from immune non-responding patients (top, 1–13) and immune responding patients (bottom, 14–33) obtained prior to immunization were assessed for
IFN-γ-secreting immune responses by ELISPOT following stimulation with peptides pools specific to the alternative splice variants of PAP or a peptide pool from
the native antigen. The presence of a statistically significant IFN-γ-secreting immune response to a specific peptide pool as described above is indicated by an X.
PAP. A major goal for investigators in the field of cancer
immunotherapy is the identification of patient characteristics capable of predicting immune response and/or
informing vaccine target selection [35]. While we did not
find evidence of response discrimination, larger patient
population and inclusion of other somatic and tumor antigens in the sequencing step might aid in this goal. We
found a significant association between immune response
to pTVG-HP and the synonymous mutation: PAP-c
.122T>G. Others have published interesting, sometimes
deleterious, effects of synonymous coding mutations including alteration of spliceosome recognition sites, activation of cryptic splice donor sites, destabilization of
mRNA, alteration of codon preference during splicing,
modulation of mRNA degradation, and/or ribosomal
interaction during translation [36-39]. This particular
mutation occurs within the first codon of the second exon.
Hence, it is conceivable that this variant affects correct
splicing and thus might affect antigen expression overall
rather than affect a specific epitope. We were not able to
evaluate PAP protein expression in individual subjects,
however the possibility that synonymous mutations could
lead to difference in protein expression that affects immunological response provides an avenue for future studies. In addition, expanding the patient population and
perhaps including upstream promoter regions, intronic
and downstream regulatory regions, and androgen- or
immune-related genes as well as evaluating the possible
structural and interacting elements influencing this antigen are also of great future interest.
Other criteria have been reported or discussed as possibly predicting for immune response to vaccination,
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
http://www.immunotherapyofcancer.org/content/1/1/2
including the so-called “immune score,” pre-existing immune responses, and other intrinsic patient characteristics [40-42]. It is hypothesized that DNA vaccination is
facilitated by TLR9 activation by vaccine-encoded CpG
motifs. Of interest, Silver and colleagues reported that
TLR9 expression and function demonstrate responsiveness to circadian rhythm in mice [43]. As such, it is conceivable that the timing of DNA vaccination in human
patients might be scheduled to increase immunogenicity.
In addition, recent work from our lab using samples
from some of these same patients, showed that PAPspecific T-regulatory cells expressing CTLA-4 and secreting IL-35 exist in some individuals prior to vaccination and persist during immunization [44]. This
suggests that the detection of antigen-specific regulatory
T-cell responses might be an additional means of identifying patients likely to respond, or not, to vaccination.
The present study examines baseline genomic, transcriptional, and immunological differences in a protein
target antigen (PAP) against which study patients eventually were vaccinated with a genetic vaccine. The field
of cancer immunotherapy continues to make progress
towards elucidating the reasons or mechanisms for why
one patient responds and another does not. This study
may represent a starting point for future workflow methodologies attempting to “personalize” antigen-specific
immunization to identify which patients are most likely
(or not) to respond to immunization.
Conclusions
In this report we hypothesized that patients expressing
highly homologous allelic variants and/or alternative
splice variants of a tumor antigen (PAP) might present different epitopes than those encoded by a genetic vaccine,
thus permitting the vaccine to invoke a cross-reactive response to homologous, but potentially not “self,” epitopes.
Despite a relatively small population, we did not identify
non-synonymous amino acid coding variants within the
genomic sequences encoding this antigen, however expression of alternative PAP splice variants was common.
Neither was associated with immune outcome, effectively
demonstrating that genetic vaccination can elicit a response to the host genome-encoded antigen and that immune responses detected are not directed to “foreign”
epitopes presented during vaccination. We believe these
findings are of relevance to other anti-tumor vaccines, including sipuleucel-T, the only FDA-approved anti-tumor
vaccine that similarly targets the PAP tumor antigen.
Methods
Patient population, study agent, regulatory information,
and clinical trial information
We have previously reported the results of a Phase I trial
using a plasmid DNA vaccine encoding human PAP,
Page 10 of 13
pTVG-HP, in patients with biochemically (serum PSA) recurrent prostate cancer after definitive surgery and/or radiation therapy not receiving androgen deprivation
therapy [13,14]. A similar Phase Ib/II trial using pTVGHP is ongoing at the time of this writing, in patients with
biochemically (serum PSA) recurrent prostate cancer after
definitive surgery and/or radiation therapy, without radiographic evidence of metastases, and receiving androgen
deprivation therapy (NCT00849121). Cryopreserved peripheral blood mononuclear cell (PBMC) samples from
these two trials were prepared using the same procedures,
and used for the analyses described. In short, PBMC from
both clinical trials were purified from blood in heparinized
collection tubes generally within 6 hours of phlebotomy
appointment and were cryopreserved in liquid nitrogen.
Samples were grouped as immune responders and immune non-responders based on previous detection of
PAP-specific interferon-gamma secreting immune response up to one year following vaccination with pTVGHP by ELISPOT, as previously described [14]. Specifically,
patients with significant (p < 0.05 by two-tailed t test comparison with media-only control) PAP protein-specific
IFNγ response detectable at two or more time points over
one year following vaccination were designated as immune responders. Patients not meeting these criteria were
designated immune non-responders. Multiple vials from
each patient in either response pool were effaced to remove identification and then recoded numerically to
maintain anonymity. Study procedures were reviewed and
approved by the Institutional Review Board of the University of Wisconsin-Madison.
Written informed consent was obtained from all patients for use of blood samples for research remaining
from the clinical trials, and the specific research of this
report was approved by the IRB of the University of
Wisconsin-Madison.
Genomic DNA extraction, primer design, PCR
amplification, and direct Sanger sequencing
Somatic, genomic DNA was extracted from cryopreserved
PBMC samples using Wizard Genomic DNA Extraction
Kit (Promega, Madison, WI, USA) per the manufacturer’s
instructions. DNA samples were quantified by Nanodrop
spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). PCR amplification and sequencing
genomic DNA oligonucleotide primers were designed
for ten exons of PAP (ACPP-001, Ensembl Gene ID:
ENSG00000014257) and five exons of PSA (KLK3-201,
Ensembl Gene ID: ENSG000000142515) from genomic
sequence data available (Additional file 1: Table S1). Samples were sequenced at the University of Wisconsin Biotechnology Center DNA Sequencing Core Facility using
described primers by the direct Sanger method [45]. Sequence data were retrieved for all 15 exons from 33
Becker and McNeel Journal for ImmunoTherapy of Cancer 2013, 1:2
http://www.immunotherapyofcancer.org/content/1/1/2
patients including 5’ and 3’ sequence runs. Tracings were
viewed with FinchTV 1.3.1 (Geospiza, Seattle, WA, USA)
and chromatograms were exported, as is, to FASTA sequence file format. FASTA DNA sequences were analyzed
with DNAMAN 5.2.8 (Lynnon Corp, Pointe Claire, Quebec,
Canada). Multiple sequence alignments were created
from all patients for each sequence in both 5’ and 3’ directions, referenced to expected sequences taken from
the Ensembl database. Consistency and fidelity were crossreferenced against original tracing data and compared between 5’ and 3’ sequencing runs for each patient exon.
RNA purification, cDNA synthesis, and reversetranscriptase PCR
Messenger RNA was purified from PBMC using Qiagen
RNeasy Mini Kit (Valencia, CA, USA) according to the
manufacturer’s instructions. RNA samples were quantified by Nanodrop spectrophotometer. RTPCR using the
Qiagen One-Step RT-PCR Kit was performed as previously described using collected mRNA from patient
samples and primers indicated in Additional file 2:
Table S2 [46]. Briefly, the following reaction conditions
were used: 50°C for 30 minutes, 95°C for 15 minutes,
35 cycles of 95°C for 1 minute, specific annealing
temperature of 60°C for 1 minute, and 72°C for 1 minute, and a final extension of 72°C for 10 minutes. Reaction products were then separated and evaluated by
agarose gel electropheresis. Amplified product bands
were isolated from agarose gel using Qiaquik Gel Extraction Kit (Qiagen) and collected DNA samples were
sequenced for confirmation.
Peptides
Four protein-coding transcripts of PAP were aligned by
amino acid sequence using DNAMAN 5.2.8: ACPP-001
(native PAP, Ensembl Transcript ID: ENST00000336375),
ACPP-002 (ENST00000475741), ACPP-003 (ENST00000
351273), and ACPP-004 (ENST00000495911). 15-mer
peptides spanning splice junctions of the alternative PAP
variants were synthesized (Lifetein, South Plainfield, NJ,
USA), and were >85% in purity confirmed by highpressure liquid chromatography (HPLC) and mass spectroscopy (MS). A peptide pool (PAP1-386) comprised of 38
individual 15-mer overlapping peptides spanning the full
length of the native PAP protein (ACPP-001) was used to
identify immune responses to conserved regions of PAP
[28]. Control peptides included a 15-mer peptide
(QVYIRSTDVDRTLMS) derived from the rat PAP
homologue and a 9-mer peptide (RLRERKQLV) derived
from the human SSX-2 protein [47].
Interferon-gamma ELISPOT
Immune response to antigen stimulation was determined by 48-hour interferon-gamma (IFN-γ) ELISPOT
Page 11 of 13
assay (Thermo Fisher Scientific), using similar methodology and test antigens as previously described [14].
PBMC at 100,000 cells per well were incubated with
2 μg/μL alternative splice variant peptide pools, 2 μg/μL
control peptides, 1 μg/μL PAP1-386, and 5 μg/μL phytohemagglutinin (PHA) in eight-well replicates. The number of spots per well was determined with an automated
ELISPOT reader (AID Diagnostika GmbH, Straussberg,
Germany) and normalized to 106 starting PBMC. For
each subject, the mean number of spots detected under
media-only conditions was subtracted from the antigenspecific conditions to enumerate antigen-specific IFN-γ
spot-forming units ± standard deviation. For all patients
the median number of IFN-γ spot-forming units with
medium alone was 104 (range 9–2408) per million
PBMC. Comparison of experimental wells with control
media-only wells was performed using a two-tailed t test,
with p-value less than 0.05 used to define a significant
T-cell response.
Additional files
Additional file 1: Table S1. Genomic DNA primers for amplification
and sequencing of PAP and PSA exons.
Additional file 2: Table S2. DNA primers for amplification and
sequencing of native and/or alternative splice variants of PAP.
Abbreviations
Aa: Amino acid; CEA: Carcino-embryonic antigen; CTL: Cytotoxic Tlymphocyte; HPLC: High-pressure liquid chromatography; MS: Mass
spectrometry; NSCLC: Non-small cell lung cancer; PAP: Prostatic acid
phosphatase; PBMC: Peripheral blood mononuclear cells;
PHA: Phytohemagglutinin; PSA: Prostate-specific antigen; PSMA: Prostatespecific membrane antigen; SNP: Single nucleotide polymorphism;
TAA: Tumor-associated antigen.
Competing interests
The authors declare no conflict of interest.
Authors' contributions
JTB carried out the sequence analysis and experimental plan, and was
primarily responsible for the interpretation and analysis of results and
manuscript preparation. DGM conceived of the study, and participated in the
design and coordination, and helped to draft the manuscript. Both authors
read and approved the final manuscript.
Acknowledgments
This work was supported by the Department of Defense Prostate Cancer
Research Program W81XWH-05-1-0404, by the National Institutes of Health
R01 CA142608, R21 CA132267 and K23 RR16489, and by the UW Carbone
Cancer Center. We would like to thank LE Johnson and VT Colluru for their
editorial input and J Niece at the UWBC-DNA Core for technical assistance.
We would like to acknowledge JS Bach and MN Rothbard for their
intellectual inspiration.
Received: 18 December 2012 Accepted: 6 March 2013
Published: 29 May 2013
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doi:10.1186/2051-1426-1-2
Cite this article as: Becker and McNeel: Presence of antigen-specific
somatic allelic mutations and splice variants do not predict for
immunological response to genetic vaccination. Journal for
ImmunoTherapy of Cancer 2013 1:2.
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