Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors

Abstract

Background
Human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) is an emerging disease, representing a distinct clinical and epidemiological entity. Understanding the genetic basis of this specific subtype of cancer could allow therapeutic targeting of affected pathways for a stratified medicine approach.

Methods
Twenty HPV+ and 20 HPV- laser-capture microdissected oropharyngeal carcinomas were used for paired-end sequencing of hybrid-captured DNA, targeting 3,230 exons in 182 genes often mutated in cancer. Copy number alteration (CNA) profiling, Sequenom MassArray sequencing and immunohistochemistry were used to further validate findings.

Results
HPV+ and HPV- oropharyngeal carcinomas cluster into two distinct subgroups. TP53 mutations are detected in 100% of HPV negative cases and abrogation of the G1/S checkpoint by CDKN2A/B deletion and/or CCND1 amplification occurs in the majority of HPV- tumors.

Conclusion
These findings strongly support a causal role for HPV, acting via p53 and RB pathway inhibition, in the pathogenesis of a subset of oropharyngeal cancers and suggest that studies of CDK inhibitors in HPV- disease may be warranted. Mutation and copy number alteration of PI3 kinase (PI3K) pathway components appears particularly prevalent in HPV+ tumors and assessment of these alterations may aid in the interpretation of current clinical trials of PI3K, AKT, and mTOR inhibitors in HNSCC.

Full text

RESEARCH Open Access
Targeted next-generation sequencing of head
and neck squamous cell carcinoma identifies
novel genetic alterations in HPV+ and
HPV- tumors
Matthias Lechner
1,2†
, Garrett M Frampton
3†
, Tim Fenton
1
, Andrew Feber
1
, Gary Palmer
3
, Amrita Jay
4
,
Nischalan Pillay
1
, Martin Forster
1,2
, Maureen T Cronin
3
, Doron Lipson
3
, Vincent A Miller
3
, Timothy A Brennan
3
,
Stephen Henderson
1
, Francis Vaz
2
, Paul O’Flynn
2
, Nicholas Kalavrezos
2
, Roman Yelensky
3
, Stephan Beck
1
,
Philip J Stephens
3
and Chris Boshoff
1*
Abstract
Background: Human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) is an emerging
disease, representing a distinct clinical and epidemiological entity. Understanding the genetic basis of this specific
subtype of cancer could allow therapeutic targeting of affected pathways for a stratified medicine approach.
Methods: Twenty HPV+ and 20 HPV- laser-capture microdissected oropharyngeal carcinomas were used for paired-
end sequencing of hybrid-captured DNA, targeting 3,230 exons in 182 genes often mutated in cancer. Copy
number alteration (CNA) profiling, Sequenom MassArray sequencing and immunohistochemistry were used to
further validate findings.
Results: HPV+ and HPV- oropharyngeal carcinomas cluster into two distinct subgroups. TP53 mutations are
detected in 100% of HPV negative cases and abrogation of the G1/S checkpoint by CDKN2A/B deletion and/or
CCND1 amplification occurs in the majority of HPV- tumors.
Conclusion: These findings strongly support a causal role for HPV, acting via p53 and RB pathway inhibition, in the
pathogenesis of a subset of oropharyngeal cancers and suggest that studies of CDK inhibitors in HPV- disease may
be warranted. Mutation and copy number alteration of PI3 kinase (PI3K) pathway components appears particularly
prevalent in HPV+ tumors and assessment of these alterations may aid in the interpretation of current clinical trials
of PI3K, AKT, and mTOR inhibitors in HNSCC.
Background
Human papillomavirus-related (HPV+) head and neck
squamous cell carcinoma (HNSCC) is a subgroup of
HNSCC where the incidence is increasing in most devel-
oped countries [1]. The vast majority of HPV+ HNSCC
originate from the oropharynx, and in particular the ton-
sillar beds [2]. These tumors are almost exclusively asso-
ciated with HPV-16, have integrated and functionally
active E6 and E7 viral oncoproteins, and compared to
HPV-negative tumors appear to have an overall better
outcome, independent of treatment modality [3].
Whole-exome sequence analysis was previously per-
formed to reveal the mutational landscape of HNSCC
[4,5]. These studies showed that >80% of tumors contain
TP53 mutations and strikingly up to 20% have loss-of-
function NOTCH1 mutations. However, in these two stu-
dies, only seven and four HPV+ samples were included,
respectively. Both studies confirmed the lack of TP53
mutations compared to HPV- samples, and overall, a
lower mutational burden in HPV+ disease.
* Correspondence: c.boshoff@ucl.ac.uk
†Contributed equally
1
UCL Cancer Institute, University College London, 72 Huntley Street, London,
WC1E 6BT, UK
Full list of author information is available at the end of the article
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© 2013 Lechner et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creative commons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, pro vided the original work is properly cited.

To further understand the contribution of somatic
genomic alteration in the pathogenesis of HPV+ HNSCC
we employed paired-end sequencing of hybrid-captured
DNA, targeting 3,230 exons in 182 of the most common
cancer-altered genes, plus 37 introns from 14 genes often
rearranged in cancer.
Methods
Sample collection, p16 staining, and DNA extraction
Ethicalapprovalforthisstudy was granted by the UCL/
UCLH Ethics Committee (Reference number 04/Q0505/
59) with informed consent obtained where required. Based
on the results of a power analysis and taking into account
gender and age-matching requirements we selected
20 HPV+ and 20 HPV- oropharyngeal carcinomas (from
22 HPV+ and 34 HPV- oropharyngeal cancer samples
available to us), all formalin fixed paraffin-embedded
(Table 1). Our power analysis suggested that by choosing
the described number of samples there was a just under
90% chance of detecting moderate differences in the pro-
portion of mutations between HPV+ and HPV- HNSCC
samples (w = 0.5, P= 0.05).
Details of sample preparation and selection are illu-
stratedinFigure1.WeconfirmedHPVstatusbyp16
staining, and by quantitative PCR for HPV-16 E6, having
been shown to have 97% sensitivity, 94% specificity, and
to be the best discriminator of favorable outcome [6].
Sequencing of HPV DNA demonstrated 100% concor-
dance of HPV status. All samples were laser-capture
microdissected (LCM) to separate tumor epithelial from
surrounding stromal tissues, enriching tumor DNA for
further analyses. These were processed as 10 μmthick
unstained slides which were reviewed by an expert
pathologist who had marked the slides for tumor subtype
enrichment in a corresponding H&E stained section.
LCM was carried out on P.A.L.M. MembraneSlide 1.0
PEN slides (Zeiss Microimaging, Munich, Germany)
using the Zeiss Palm MicrobeamTM system. Tissue was
collected into extraction tubes and processed using the
QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Ger-
many). Extracted DNA was quantified using a standar-
dized PicoGreen fluorescence assay (LifeTechnologies,
Carlsbad, CA, USA).
DNA library construction and hybrid capture
At least 50 ng and up to 200 ng of extracted DNA was
sheared to approximately 100-400 bp by sonication, fol-
lowed by end-repair, dA-addition and ligation of indexed,
Illumina sequencing adaptors. Sequencing libraries were
hybridization captured using RNA-based baits (Agilent),
targeting a total of 3,320 exons of 182 cancer-related
genes (most commonly altered in cancer, from [7]) plus
37 introns from 14 genes often rearranged in cancer
(Additional File 1, Table S1).
Table 1 Patient characteristics of selected HPV+ and HPV- HNSCC samples.
HPV+ (n= 20) HPV- (n= 20)
Median age, years (range) 56.5 (42-81) 58 (45-77)
Gender M: 14 M: 14
F: 6 F: 6
Tumor site Oropharynx: 20 Oropharynx: 20
Tumor grade Well diff: 1 Well diff: 0
Mod diff: 9 Mod diff: 16
Poorly diff: 10 Poorly diff: 4
Tumor stage (T) T1: 5 T1: 1
T2: 8 T2: 4
T3: 3 T3: 5
T4: 3 T4: 10
N/a: 1 N/a: 0
Cervical lymph node involvement (N) Yes: 16 Yes:13
No: 2 No: 6
N/a: 2 N/a: 1
Smoking Ever: 9 Ever: 15
Never: 8 Never: 0
N/a: 3 N/a: 5
Alcohol Heavy drinker (>20U/w): 2 Heavy drinker (>20U/w): 12
Occ. alcohol: 5 Occ. alcohol: 3
Never: 4 Never: 0
N/a: 9 N/a: 5
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Sequencing and primary sequence data analysis
Paired end sequencing (49 × 49 cycles) was performed
using the HiSeq2000 (Illumina). Six samples yielded insuf-
ficient numbers of reads and were excluded from analysis.
The summary of sequencing details is illustrated in Addi-
tional File 1, Table S2. Sequence data from gDNA, avail-
able from 18 HPV+ and 16 HPV- samples, were mapped
to the reference human genome (hg19) using the BWA
aligner [8]. PCR duplicate read removal and sequence
metric collection was performed using Picard [9] and
SAMtools [10]. Local alignment optimization was per-
formed using GATK [11]. Hybrid capture reagents
included baits designed to capture unique regions of select
viral genomes including HPV-16. Sequence read pairs
were aligned to the reference genome of the respective
viral genomes, and the number of pairs mapping to each
viral genome was counted. A total HPV-16 aligned read
count of ≥5 reads per million was considered a positive
HPV status, and ≤2 negative HPV status.
Genomic alteration detection
Base substitution detection was performed using a
Bayesian methodology, which allows detection of
novel somatic mutations at low MAF and increased sen-
sitivity for mutations at hotspot sites [12] through the
incorporation of tissue-specific prior expectations:
P(Mutation present|Read da ta ”R”) = P(Frequency of mutation ”F” >0|R)∝1−P(R|F=0)P(F=0)
,
where P
(
R|F
)
is evaluated with a multinomial distribution
Figure 1 Workflow of FFPE sample preparation and selection. Eighty-two FFPE blocks [19] were stained for p16 of which eight samples were
excluded from further analysis, showing mixed p16 staining. Eight samples were excluded after the LCM step, yielding insufficient amounts or quality
of DNA and two further samples were excluded due to inconsistent or borderline results in repeat E6 qPCR measurements. In total, 22 confirmed HPV
+ (p16+ and E6 qPCR+) and 34 HPV- (p16- and E6 qPCR-) samples were suitable for further analysis. Following age and gender matching, 20 HPV+
HNSCC samples (red) and 20 HPV- HNSCC samples (grey) were then selected for the final analysis (next-generation (NG) sequencing).
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of the observed allele counts using empirically observed
error rates and P
(
F=0
)
is the prior expectation of muta-
tion in the tumor type. To detect indels, de-novo local
assembly in each targeted exon was performed using the
de-Bruijn approach [13]. Candidate calls are filtered
using a series of quality metrics, including strand bias,
read location bias, and a custom database of sequencing
artifacts derived from normal controls. Germline altera-
tions are identified and filtered using dbSNP (version 135
[14]) and subsequently annotated for known and likely
somatic mutations using the COSMIC database (version
62, http://cancer.sanger.ac.uk/cancergenome/projects/
cosmic/). Detection of copy-number alterations (CNAs)
was performed by obtaining a log-ratio profile of the
sample by normalizing the sequence coverage obtained at
all exons against a process-matched normal control. The
profile is segmented and interpreted using allele frequen-
cies of ~1,800 additional genome-wide SNPs to estimate
tumor purity and copy number based on established
methods [15-17] by fitting parameters of the equation
lrseg ∼N(log2
p∗Cseg +(1−p)∗2
p∗tumor ploidy +
(
1−p
)
∗2
)
,wherelrse
g
,
Cse
g
,andpare the log-ratios and copy numbers at each
segment and sample purity respectively. Focal amplifica-
tions are called at segments with ≥6copiesandhomo-
zygous deletions at 0 copies, in samples with purity
>20%.
A summary of known and likely somatic or functional
base substitution and indel (short-variant) alterations
and of base substitution and indel (short-variant) altera-
tions of unknown status detected by deep sequencing is
illustrated in Additional File 1, Table S3 and Additional
File 1, Table S4, respectively. A summary of copy num-
ber alterations detected by deep sequencing is illustrated
in Additional File 1, Table S5.
Validation of selected mutations by Sequenom OncoCarta
DNA extracted from FFPE samples were sent to Sequenom
(Hamburg, Germany) for blind testing and analysis, using
Sequenom OncoCarta panels v1.0 and v3.0, as previously
described [18].
Confirmation of copy number changes by Infinium CNA
profiling
Using previously obtained Infinium HumanMethylation
450 BeadChip methylation data on sequenced samples
[19], the Bioconductor package ‘DNAcopy’[20,21] was
applied to calculate the copy number of the majority of
sequenced samples, as described previously [22]. All
normalized and raw 450k methylation data were sub-
mitted to GEO (Gene Expression Omnibus, NCBI)
according to instructions provided (GEO accession
number: GSE38266).
Immunohistochemistry and interpretation of results
The sequenced 18 HPV+ and 16 HPV- HNSCC samples
were stained for PTEN and for Cyclin D1. Staining for
these particular targets was chosen as these were already
implicated in HNSCC carcinogenesis and validated scor-
ing systems are available [23,24]. Antibody 04-409 (Milli-
pore-Merck KGaA, Darmstadt, Germany) was used for
PTEN staining and antibody P2D11F11 (Novocastra) was
used Cyclin D1 staining of 10-μm thick slides. The
stained slides were examined and scored as previously
described [23,24] by two experienced histopathologists.
Statistical data analysis
Significance of enrichment of observed genomic altera-
tions in HPV+ and HPV- HNSCC cases was tested using
Pearson’s chi-squared test. Relation of gender, tumor site,
tumor grade, size of primary tumors (T), lymph node
metastasis (N), smoking status, and alcohol intake to the
two tested groups was determined using the Wilcoxon
rank sum test. Relation of age to the two groups was
testedbyalogisticregressionmodel.Theobtained
Pvalues were corrected for multiple testing (FDR adjust-
ment). Correlation of sequencing results with CCND1 and
PTEN immunochemistry was tested using Fisher’s exact
test.
Results
Patient demographic data
The median age is slightly higher in the HPV- group (58
vs. 56.5 years) (Table 1). The male to female ratio is similar
between the groups, and the majority of cases show mod-
erately or poorly differentiated histology with evidence of
lymph nodal involvement at presentation. In our cohort,
as predicted, the vast majority of HPV- cases are in active
smokers and/or heavy alcohol users (Table 1 and Figure 2).
No significant relationship of gender, tumor site, tumor
grade, size of primary tumors (T), lymph node metastasis
(N), smoking status, determined using the Wilcoxon rank
sum test, to any of the two tested groups (HPV+ HNSCC
vs. HPV- HNSCC) was seen. Patients with high alcohol
intake were significantly enriched in the HPV- group
(Wilcoxon rank sum test; adjusted Pvalue <0.05).
Next-generation sequencing
Sequence analysis revealed that HPV+ and HPV- orophar-
yngeal carcinomas cluster into two distinct subgroups,
with few overlapping genetic alterations (Figures 2 and 3).
TP53 mutations are detected in 100% of HPV- samples
(Figure 2; significant enrichment in HPV- group; chi-
square test, q <0.01). The list of observed TP53 mutations
is illustrated in Additional File 1, Table S6. CCND1
amplifications (chi-square test, q <0.01) and CDKN2A/B
deletions (chi-square test, q <0.05) were exclusively
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detected in HPV- cases (in approximately 55% and 40%
of cases). PIK3CA mutation or amplification, and PTEN
inactivation by gene copy loss or mutation were seen in
>55% of HPV+ tumors, and in 31% HPV- tumors. FBXW7
alterations were present in >15% of all samples and SOX2
amplification in 12% of cases.
Validation of obtained results
For validation of our results, we applied Infinium CNA pro-
filing, Sequenom OncoCarta panels v1.0 and v3.0 and
immunohistochemistry. Copy number gains and losses
detected by next-generation sequencing (NGS) were inter-
rogated by Infinium CNA profiling (Additional File 2,
Figure S1). Forty-eight of fifty (96%) copy number altera-
tions detected by sequencing were confirmed (Figure 4).
Furthermore, the detected mutations by NGS were
validated by Sequenom OncoCarta panels v1.0 and v3.0
(Additional File 2, Figure S2). As our NGS technique
targeted the whole gene sequence, whereas Sequenom
OncoCarta panels only target specific mutational hotspots
of certain genes, the majority of NGS detected mutations
were not included in the Sequenom analysis. Eight out of
nine mutations that were detected by NGS were also con-
firmed by Sequenom. One PIK3CA mutation in sample
P72_pos was called at 1% allele frequency by NGS, and this
mutation was therefore unlikely to be detected by Seque-
nom analysis.
For CCND1 and PTEN we also validated findings by immu-
nohistochemistry in sample material from the 18 HPV+
and 16 HPV- HNSCC samples tested by NGS. Genomic
alterations in CCND1 were confirmed by Cyclin D1 immu-
nochemistry with strong expression of Cyclin D1 protein in
eight of nine CCND1 amplified cases (and intermediate
expression in the remaining case). Using all tested samples,
significant correlation of CCND1 sequencing results with
Cyclin D1 immunochemistry was observed (P= 7.34e-05;
Fisher’s exact test). Representative samples are shown in
Figure 5. PTEN loss and mutation were validated by immu-
nohistochemistry (Figure 6). PTEN staining was negative in
all cases in which NGS revealed a homozygous deletion or
mutation. Four additional samples displayed low PTEN
protein expression. In three of these cases a heterozygous
deletion/single copy loss of PTEN was present, as detected
by NGS. In the remaining sample other mechanisms may
Site
Smoking
Alcohol
% mutated sa mples
TP53 50%
PIK3CA 34%
CCND1 27%
CDKN2A 27%
CDKN2B 21%
PTEN 15%
FBXW7 15%
SOX2 12%
EGFR 6%
MYC 6%
KRAS 6%
BCL2L1 6%
RICTOR 6%
CCND3 3%
MDM2 3%
TET2 3%
SUFU 3%
PKHD1 3%
LRP1B 3%
FGFR1 3%
FGFR3 3%
KDM6A 3%
MCL1 3%
NOTCH1 3%
STK11 3%
RB1 3%
P6_pos
P8_pos
P13_pos
P19_pos
P26_pos
P28_pos
P35_pos
P38_pos
P43_pos
P50_pos
P60_pos
P67_pos
P72_pos
P74_pos
P79_pos
P82_pos
P83_pos
P105_pos
P7_neg
P10_neg
P12_neg
P14_neg
P17_neg
P24_neg
P25_neg
P29_neg
P40_neg
P62_neg
P70_neg
P90_neg
P91_neg
P92_neg
P94_neg
P95_neg
GeneƟc changes de tected
Focal ampliĮcaƟon
Homozygous deleƟon
Muta Ɵon
Focal ampliĮcaƟon & mutaƟon
Tumor Si te
Tonsi l
Base of tongue
Smoking status
No tobacco exposure
Ex-s moker
AcƟve smoker
Unkn own
Alcohol intake
No alcohol intake
Occ. al cohol i ntake
>24 U alc ohol /we ek
Unkn own
HPV stat us
HPV p osiƟve
HPV n egaƟve
F
i
g
ure 2
Figure 2 Illustration of somatic events in HPV+ and HPV- HNSCC revealed by NGS of cancer-related genes. Relevant demographic and
histological data are described above the heatmap of genomic changes. The color coding of the observed changes and patient characteristics
are explained in the key on the right.
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explain the loss of expression, such as an epigenetic altera-
tion or changes in the post-transcriptional regulation of
PTEN. Overall highly significant correlation of PTEN
sequencing results with PTEN immunochemistry was
demonstrated (P= 0.0009; Fisher’s exact test).
Mutations reported in this study as ‘known somatic’
were limited to those that have been previously confirmed
to be somatic in other tumors, through sequencing of
matched normal specimens. Consequently, we are confi-
dent that these alterations are somatic.
A
Figure 3 Hierarchical clustering of HPV+ and HPV- HNSCC samples using all detected genetic changes. HPV+ and HPV- HNSCC samples
clustered in 100% of cases.
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Discussion
Overall, sequence analysis revealed that HPV+ and HPV-
oropharyngeal carcinomas cluster into two distinct sub-
groups, with few overlapping genetic alterations. These
data concur with epidemiological and clinical data,
indicating that HPV+ HNSCC is a distinct disease entity
[25,26].
Our detection of TP53 mutations in 100% of HPV-
samples, higher than previously reported [27], suggests that
our approach of laser capture microdissection coupled
HPV s tatus
CCND1 GGGGGG GGG
CCND3 G
CDKN2A LLLLLL L L
CDKN2B LLLLL L L
EGFR GG
MDM2 G
TET2
SUFU
PKHD1
LRP1B
FGFR1 G
KDM6A L
MYC GG
MCL1 G
RICTOR GG
BCL2L1 GG
SOX2 GGGG
PTEN LLL
FBXW7 L
PIK3CA GGGGG
P6_pos
P8_pos
P13_pos
P19_pos
P26_pos
P28_pos
P35_pos
P38_pos
P43_pos
P50_pos
P60_pos
P67_pos
P72_pos
P74_pos
P79_pos
P82_pos
P83_pos
P105_pos
P7_neg
P10_neg
P12_neg
P14_neg
P17_neg
P24_neg
P25_neg
P29_neg
P40_neg
P62_neg
P70_neg
P90_neg
P91_neg
P92_neg
P94_neg
P95_neg
Region of gain within
chromosome 11
(CCND1 amplication)
Region of loss within
chromosome 9
(CDKN2A & CDKN2B loss
)
Copy number changes across all chromosomes
911
Sample P17_neg
BC
TP53
PIK3CA
CCND1
CDKN2A
CDKN2B
SOX2
PTEN
FBXW7
EGFR
NF1
KRAS
BCL2L1
CCND3
MDM2
TET2
SUFU
PKHD1
LRP1B
FGFR1
FGFR3
KDM6A
MYC
MCL1
RICTOR
STK11
RB1
P17_neg
A
Sample P17_neg
Copy number gain
Copy number loss
Muta Ɵon
Figure 4 Validation of copy number changes by Infinium CNA profiling across all samples.(A) Forty-eight of 50 (96%) copy number
alterations detected by sequencing were confirmed (green: confirmed, pink: not confirmed, grey: no data); (B) Genetic changes in ‘P17_neg’detected
by NGS (extracted from Figure 2); (C) Illustration of copy number changes (obtained from Infinium CNA Profiling) in ‘P17_neg’. Both the loss of the
CDKN2A and CDKN2B genes (in a region of loss within chromosome 9) and the gain of the CCND1 gene (in an amplified region of chromosome 11)
are shown. Y-axis: log fold change of copy number, X-axis: copy number changes across all chromosomes.
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with targeted deep sequencing is a highly sensitive method
bywhichtoassayspecifictumormutations.Taken
together with the fact that in the HPV+ tumors, p53 func-
tion is suppressed by E6, our data suggest an obligate
requirement for p53 abrogation in oropharyngeal tumori-
genesis. One caveat in our study is that all HPV- samples
analyzed were also p16 negative, thus it remains possible
that in HPV- samples with elevated p16 expression (for
example, through RB1 mutation), the frequency of TP53
mutation is <100%.
We identified only one TP53 mutation in an HPV+
tumor. However, this mutation (R290C, Additional File 1,
Table S2) causes only a 40% decrease in TP53 function
and has been detected in sarcomas harboring MDM2
amplification [28,29].
Our data for HPV- oropharyngeal cancer indicate that
the frequency of CCND1 amplification (in approximately
55% of cases) and CDKN2A/B deletions (in approximately
55% of cases) are higher than previously reported [30].
CCND1 amplification has also been described in 12% of
non-small cell lung cancers [31] and in up to 41% of eso-
phageal squamous cell carcinomas [32], suggesting that
this could be one of the more common genetic alterations
linked to smoking-induced epithelial malignancy. In HPV
+ cancer, the oncoprotein E7 leads to cell cycle dysregula-
tion by substituting for cyclin D gain-of-function and
cyclin dependent kinase inhibitor loss-of-function activ-
ities. Overall, this indicates that direct dysregulation of the
cell cycle is a key mechanism for oropharyngeal tumors to
evolve.
HPV+ HNSCC samples frequently harbor mutations or
CNAs in genes implicated in activation of the PI3K/AKT/
mTOR pathway. In particular, PIK3CA mutation and
PTEN inactivation by gene copy loss or mutation were
A B
C D
Figure 5 Validation of detected copy number alterations of Cyclin D1 (CCND1) by immunohistochemistry. Staining of HNSCC samples for
Cyclin D1 confirmed strong expression in eight of nine CCND1 amplified cases (and intermediate expression in the remaining case) compared
with samples harboring no copy number alteration; Representative samples shown: Low levels of CCND1 expression in the tumor tissue of
sample ‘P38_pos’(A) and sample ‘P29_neg’(B); NGS: No CNA; High levels of Cyclin D1 expression in the tumor tissue of sample ‘P12_neg’
(C) and sample ‘P17_neg’(D); NGS: CCND1 copy number gain.
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seen in >60% of HPV+ tumors, and in 31% HPV- tumors.
There is a significant relation between PIK3CA and
PTEN, and HPV status; chi-square test, P<0.001. These
findings may help to explain the high frequency of PI3K
pathway activation in HPV+ HNSCC samples and the effi-
cacy of mTOR inhibitors in xenograft studies with HPV+
cell lines previously reported [33]. It will be important to
audit both the sequence and copy number of the PIK3CA
and PTEN genes if such agents are tested in clinical trials
for HPV-associated HNSCC.
Our results suggest that mutations in FBXW7 may be
enriched in HPV+ disease. FBXW7 is an E3 ubiquitin
ligase that targets a number of growth-promoting proteins
for proteasomal degradation, including Cyclin E, MYC,
NOTCH and mTOR [34,35]. Loss of FBXW7 occurs in
combination with NOTCH gain-of-function mutations in
T-ALL [36], suggesting it may be an important target for
FBXW7 ligase activity in these tumors. In contrast,
HNSCC frequently display NOTCH loss-of-function-
mutations [37,38], thus in HNSCC, other substrates such
as Cyclin E, MYC, or mTOR may be the relevant targets
forFBXW7.WefoundoneHPV-sampleharboringa
NOTCH1 mutation, concurring with previous studies
reporting NOTCH1 mutations in HNSCC [4,5].
Two of our tested HPV+ samples harbored KRAS muta-
tions. KRAS mutations have been associated with a history
of smoking [39]. One of the patients was a smoker and in
the other one the smoking status was unknown. HRAS
mutations were not detected in any of our tested samples.
In previous studies, mutations in the HRAS gene were
mainly detected in oral cavity cancer samples [4,5].
The SOX2 and PIK3CA genes both reside on the long
arm of chromosome 3 (3q26) and these genes were ampli-
fied in three HPV+ samples and one HPV- tumor. While
PIK3CA amplifications have previously been reported in
HPV+ HNSCC [40,41], SOX2 has recently been proposed
A B
C D
Figure 6 Validation of detected PTEN copy number loss by immunohistochemistry. Staining of HNSCC samples for PTEN was negative in
all cases in which deep sequencing revealed a homozygous deletion or mutation. Representative samples shown: Abundant PTEN expression in
the tumor tissue of sample ‘P26_pos’(A) and sample ‘P70_neg’(B); Deep-sequencing: No CNA; Absence of PTEN protein in the tumor tissue of
sample ‘P60_pos’(C) and sample ‘P13_pos’(D); Deep-sequencing: PTEN copy number loss.
Lechner et al.Genome Medicine 2013, 5:49
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as the critical target of 3q gains observed at a high fre-
quency in squamous lung cancer [42] and in esophageal
squamous cell carcinoma [43]. SOX2 is also frequently
amplified and overexpressed in oral squamous cell carci-
noma [44]. Furthermore, SOX2 expression is upregulated
in a subpopulation of putative HNSCC stem cells that dis-
plays characteristics of epithelial to mesenchymal transi-
tion (EMT), associated with increased propensity for
metastasis [45].
We also demonstrate for the first time inactivating
mutations in STK11 in HPV+ HNSCC. Loss of STK11 is
associated with metastasis in head and neck cancer [46].
Furthermore, loss of function mutations in STK11 (LKB1)
result in activation of mTORC1 signaling and can sensitize
cells to mTOR inhibition [47,48]. Mutations in these genes
therefore (in addition to PIK3CA and PTEN) warrant eva-
luation as potential determinants of sensitivity to mTOR
inhibitors currently in clinical trials for HNSCC [49].
Beyond the genes directly involved in signaling and cell
cycle, we found amplifications in genes implicated in pre-
venting apoptosis: BCL2L1 (6% amplification) and MCL1
(3% amplification), suggesting that direct suppression of
apoptosis may also contribute to HNSCC pathogenesis.
Receptor tyrosine kinase mutations, FGFR1, FGFR3,
and EGFR, were only observed in HPV- tumors at low
frequency.
Overall, our data strongly support a causal role for HPV
in oropharyngeal carcinogenesis by overcoming the require-
ment for genetic lesions in the TP53 and RB1 tumor sup-
pressor pathways evident in the HPV- tumors. Our
detection of frequent PI3K/AKT/mTOR pathway altera-
tions in HPV+ tumors is consistent with a recent report
demonstrating PI3K pathway activation and sensitivity to
mTOR inhibition in both cervical carcinoma and HPV+
HNSCC [33]. Together, these studies provide a rationale for
the testing of PI3K pathway inhibitors in HPV+ HNSCC. In
HPV- tumors, the frequent alteration of CDKN2A/B and/or
CCND1 suggests that, if supported by functional data, trials
with CDK inhibitors may be indicated. Our data support
the observations by gene expression microarrays and by
genome-wide methylation studies that HPV+ HNSCC is a
distinct entity, with a distinct set of somatic alterations.
However,itwouldappearthatacoresetofpathways
(TP53, RB1/cell cycle, and PI3K/AKT/mTOR) is compro-
mised in both HPV+ and HPV- oropharyngeal tumors, thus
targeted therapies directed against one or more of these
pathways could be efficacious in both contexts.
Additional material
Additional file 1: Table S1: 182 genes sequenced across entire
coding sequence (A) and 14 genes sequenced across selected
introns (B). Table S2: Summary of sequencing details for study samples.
Table S3: Summary of known and likely somatic or functional base
substitution and indel (short-variant) alterations detected by deep
sequencing. Table S4: Summary of base substitution and indel (short-
variant) alterations of unknown status detected by deep sequencing.
Table S5: Summary of copy number alterations detected by deep
sequencing. Table S6: List of TP53 mutations revealed by deep
sequencing in HPV+ and HPV- HNSCC samples.
Additional file 2: Figure S1: Infinium CNA profiling of HPV+ and
HPV- HNSCC samples. Obtained genome-wide copy number alteration
profiles (cumulative frequencies) between the two groups are illustrated
and chromosomes displaying similar patterns of gain and loss in HPV+
and HPV- HNSCC samples are boxed. Chromosome 6 (MHC regions) and
Y chromosome are not shown. Figure S2: Validation of detected
mutations by SequenomOncoCarta panels v1.0 and v3.0. Mutations in
HNSCC samples detected by deep sequencing were validated using the
OncoCartapanels v1.0 and v3.0. 8 out of 9 mutations that were
successfully tested on the Oncocarta panel were confirmed (green:
confirmed, pink: not confirmed, grey: n/a). *The PIK3CA_E545K mutation
in sample P72_pos was called at 1% allele frequency by NGS, and this
mutation was therefore unlikely to be detected by Sequenom analysis.
Abbreviations
CNA: Copy number alteration; EMT: epithelial to mesenchymal transition; FF:
fresh-frozen; FFPE: formalin-fixed paraffin-embedded; GEO: Gene Expression
Omnibus; HNSCC: head and neck squamous cell cancer; HPV: human
papillomavirus; HPV+: HPV positive; HPV-: HPV negative; LCM: laser-capture
microdissected; NGS: next-generation sequencing; PI3K: PI3 kinase.
Competing interests
NGS of samples was in collaboration with Foundation Medicine.
Employees of Foundation Medicine: GF, MTC, DL, VAM, RY, PJS
Authors’contributions
All authors contributed to the interpretation of data and to the writing of
the manuscript. In detail: Study design and conceptualization of study: ML,
GF, TF, GP, SB, CB; Sample preparation, tumor collection, and technical work:
ML, GF, TF, MF, FV, PO’F, NK; Histology and Computational Biology: AJ, AF,
TAB, RY, NP, PJS; Figures and Tables: ML, GF, TF, AF. All authors read and
approved the final manuscript.
Acknowledgements
We would like to thank Keith Miller, Mike Gandy, and Philippa Jones from
UCL Advanced Diagnostics and Dr. Geoff Boxer, George Chennell (UCL
Genomics), and the teams at the Head and Neck Centre and the
Department of Histopathology at University College London Hospitals
(UCLH) for advice and technical support.
This study was supported by the UCLH/UCL NIHR Biomedical Research
Centre (BRC) and ML was supported by a Wellcome Trust Fellowship
(WT093855MA) and by the Austrian Science Fund (J2856). SB was supported
by the Wellcome Trust (WT084071) and a Royal Society Wolfson Research
Merit Award (WM100023). The CB Laboratory is supported by Cancer
Research U.K.
Authors’details
1
UCL Cancer Institute, University College London, 72 Huntley Street, London,
WC1E 6BT, UK.
2
Head and Neck Centre, University College London Hospitals
NHS Trust, Euston Road, London, NW1 2PG, UK.
3
Foundation Medicine, One
Kendall Square, Suite B3501, Cambridge, MA 02139, USA.
4
Department of
Histopathology, University College London Hospitals NHS Trust, Rockefeller
Building, University Street, London, WC1E 6JJ, UK.
Received: 20 February 2013 Revised: 15 April 2013
Accepted: 29 May 2013 Published: 29 May 2013
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doi:10.1186/gm453
Cite this article as: Lechner et al.: Targeted next-generation sequencing
of head and neck squamous cell carcinoma identifies novel genetic
alterations in HPV+ and HPV- tumors. Genome Medicine 2013 5:49.
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