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. 2019 Nov 14;42(3):526–542. doi: 10.1590/1678-4685-GMB-2018-0005

Mutational landscape of head and neck squamous cell carcinomas in a South Asian population

Kulsoom Ghias 1,*, Sadiq S Rehmani 2,*, Safina A Razzak 3, Sarosh Madhani 4, M Kamran Azim 5, Rashida Ahmed 3, Mumtaz J Khan 6
PMCID: PMC6905448  PMID: 31188922

Abstract

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type globally and contributes significantly to burden of disease in South Asia. In Pakistan, HNSCC is among the most commonly diagnosed cancer in males and females. The increasing regional burden of HNSCC along with a unique set of risk factors merited a deeper investigation of the disease at the genomic level. Whole exome sequencing of HNSCC samples and matched normal genomic DNA analysis (n=7) was performed. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine frequently affected signaling pathways. We identified significant, novel recurrent mutations in ASNS (asparagine synthetase) that may affect substrate binding, and variants in driver genes including TP53, PIK3CA, FGFR2, ARID2, MLL3, MYC and ALK. Using the IntOGen platform, we identified MAP kinase, cell cycle, actin cytoskeleton regulation, PI3K-Akt signaling and other pathways in cancer as affected in the samples. This data is the first of its kind from the Pakistani population. The results of this study can guide a better mechanistic understanding of HNSCC in the population, ultimately contributing new, rational therapeutic targets for the treatment of the disease.

Keywords: Head and neck squamous cell carcinoma (HNSCC), whole exome sequencing, driver mutation, novel mutation, Pakistani population

Introduction

Head and neck squamous cell carcinomas (HNSCC), which include tumours of the oral cavity, oropharynx, hypopharynx and larynx, are the sixth most common cancer worldwide with a global incidence of ~600,000 cases (Jemal et al., 2005, 2011; Hayat et al., 2007; Murar and Forastiere, 2008; Ferlay et al., 2011). In Pakistan, a developing country in South Asia, HNSCC is among the most commonly diagnosed cancers in both males and females (Bhurgri et al., 2006; Masood et al., 2015). The major risk factors for HNSCC include tobacco use, alcohol consumption, and human papilloma virus (HPV) infection (Leemans et al., 2018).

HPV-negative disease accounts for ~80% of the HNSCC cases (Leemans et al., 2011). Unlike developed countries, the incidence of HPV-negative disease has steadily increased in developing countries (Leemans et al., 2011). The increased incidence in both males and females in Pakistan can be attributed to the prevalence of traditional risk factor such as smoking. The use of smokeless tobacco, betel nut, gutka (a preparation of crushed areca nut, tobacco, slaked lime and other flavorings) and betel quid or paan (a preparation of betel leaf, areca nut and occasionally tobacco) along with its related products are additional risk factors in this part of the world (Gupta and Johnson, 2014; Khan et al., 2014; Li et al., 2014).

HNSCC is associated with considerable disease-related mortality and treatment-related morbidity (Forastiere et al., 2001) and is a major public health concern for Pakistan (Bhurgri et al., 2002; Bhurgri 2004, 2005; Warnakulasuriya 2009; Bray et al., 2012) and worldwide. Despite the advances in all the major treatments for HNSCC including surgery, radiotherapy and chemotherapy, the mortality rate is ~50% (Laramore et al., 1992; Leemans et al., 2018). The existing literature focuses primarily on HNSCC in North American and European populations. There is a dearth of information specific for the South Asian population. The unique set of population-specific risk factors, germline variability and molecular heterogeneity of HNSCC demands a thorough molecular profiling of these tumours in this population in order to understand tumour progression, and identify actionable targets for therapy, leading to improved patient care. The aim of the study described here was to identify the global genetic aberrations underlying HPV-negative HNSCC in the South Asian (Pakistani) population.

Materials and Methods

Ethics approval and consent to participate

The Aga Khan University Ethics Review Committee approved the procedures used in collecting and processing of participant material and information (reference #: 1003-Sur/ERC-08). Written informed consent to participate was obtained from all subjects.

Sample collection

Fresh tumour tissue and matched blood were obtained from treatment-naïve patients undergoing surgical resection of HNSCC primary tumour at the Aga Khan University Hospital in Karachi, Pakistan. Patients with confirmed histological diagnosis of HNSCC were included in this study. At the time of resection, fresh tumour tissue away from the necrotic core measuring at least 0.5 cm2 was collected and stored in RNAlater® solution (Thermo Fisher Scientific) at -80 °C till further processing. Formalin-fixed tumour tissue samples were assessed by a histopathologist for tumour content and cellularity based on hematoxylin and eosin (H&E) staining. Seven tumour samples negative for HPV with at least 70% cancer cells and 1 μg (50 ng/μl) of extracted DNA (both tumour as well as genomic DNA) were utilized for whole exome sequencing.

DNA extraction

Genomic and tumour DNA was extracted in-house using TRIzol® Reagent (Invitrogen, USA) according to manufacturer’s instructions. Tumour DNA was extracted from at least 50 mg of tissue and genomic DNA was extracted from 3-5 mL of peripheral blood samples obtained before patients underwent surgical procedure. DNA yield and quality was assessed both in-house using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and by Macrogen Inc. (Seoul, South Korea) using PicoGreen® Assay (Invitrogen, USA).

Tumour HPV status

Formalin-fixed paraffin embedded (FFPE) tumour blocks were retrieved and DNA was extracted for assessing HPV status. PCR detection was performed using two sets of general HPV primers (GP5/GP6) (Baay et al., 1996; Khan et al., 2007). Additionally, HPV in situ hybridization (ISH) was performed on FFPE blocks using GenPoint assay according to the manufacturer’s instructions (Dako, Denmark). Dako assay can detect HPV-DNA from 13 high-risk genotypes.

Whole Exome Sequencing (WES)

WES was performed by Macrogen Inc. (Seoul, South Korea). 1-2 μg of tumour and genomic DNA was fragmented by nebulization. DNA libraries were prepared from each sample using TruSeq DNA Sample Prep Kit using the manufacturer’s protocol (Illumina, USA). Unique molecular indices were used for each sample. Exome enrichment was performed using the TruSeq Exome Enrichment kit (Illumina, USA). Paired-end sequencing was performed on Illumina HiSeq 2000 instrument. Each read was of 100 bp size.

Availability of data and materials

The data sets supporting the results of this article are included within the article and its supplementary files. The raw sequencing data of those patients that consented to deposition of data in a public database (4 out of 7 total) have been deposited in NCBI’s Sequence Read Archive and are accessible through accession number SRP083063.

Data analysis

Paired-end sequence reads from Illumina were mapped against UCSC Human Genome (hg) 19 using BWA (Li and Durbin 2009). Local realignment was performed using Genome Analysis Tool Kit (GATK) to improve mapping quality (McKenna et al., 2010). Single nucleotide variants (SNVs) were identified in both somatic and germline DNA using MuTect (high-confidence mode) with default settings. Somatic variants were defined as those SNVs which were only identified in the somatic DNA and not seen in germline DNA. Variants marked REJECT were excluded from downstream analysis. Tumour mutational burden was calculated as previously described by others (Chalmers et al., 2017). All mutations were annotated and prioritized using Variant Effect Predictor (VEP) and ANNOVAR. Further characterization of SNVs into missense, nonsense, frameshift, stop loss and stop gain variants was done using wANNOVAR, SNPEFF, SIFT and Polyphen. All somatic missense mutations were analysed for their likely tumourigenic impact based on CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) (Carter et al., 2009; Wong et al., 2011) and the IntOGen-mutations platform (Gonzalez-Perez et al., 2013). A cut-off score threshold of ≤ 0.2 for FDR with a p-value of ≤ 0.05 was applied. The annotation ranked the SNVs for somatic driver mutations for specific cancer tissue types, predicted protein functional impact, allele frequencies from the 1000 Genomes Project and ESP6500 populations, and previous cancer association of the gene harbouring the variants. CHASM training set is composed of a positive class of driver mutations from the COSMIC database and VEST training set comprising a positive class of disease mutations from the Human Gene Mutation Database 66 and a negative class of variants detected in the ESP6500 population and 1000 Genomes Project cohort with an allele frequency of >1%. SNPeff (Cingolani et al., 2012) and CHASM were used to identify stop-gain, start-loss and splice site variants in nonsynonymous coding region. Those SNVs identified by both tools were selected as significant. Mutations in non-coding regions were annotated using CADD and a cut-off threshold score of ≥15 with p<10–5 applied to predict benign and deleterious variants (Kircher et al., 2014). Pathway analysis was carried out using the IntOGen-Mutations platform (Gonzalez-Perez et al., 2013) and significantly (p≤0.05) affected pathways in the cohort and genes within identified.

ASNS protein modeling

The homology model of human asparagine synthetase was constructed using crystal structural coordinates of the enzyme from Escherichia coli (PDB id 1CT9). The Modeller program (Fiser and Sali, 2003) was used to build the asparagine synthetase model.

Results

Clinical characteristics and HPV-status of HNSCC patients

Primary tumour samples from 7 treatment-naïve HNSCC patients (Figure S1 (492.5KB, pdf) ), along with their matched genomic DNA, were used for this study. The detailed demographics and clinical characteristics of these patients are provided in Table 1. The samples were taken from five male and two female patients, who had an average age at diagnosis of 54 years (SD = 13.24). Two patients reported a family history of cancer; one patient had a personal history of smoking (110 pack years), two of oral tobacco use, one of alcohol and oral tobacco use, and four reported use of betel nut/quid. All samples were negative for human papilloma virus (Figure 1).

Table 1. Clinical characteristics of HNSCC patients. Data that is unavailable is indicated with a dash (-).

Sample ID Gender Age at diagnosis Family history of cancer (type) Smoking history Oral tobacco use Betel nut/quid use Alcohol use TNM Stage Tumour site
NM-02 M 67 Yes (brain) Yes No - No pT4N0M0 IV Left buccal mucosa
(110 pack years)
NM-08 M 35 No No Yes Yes No pT3N0M0 III Right buccal mucosa
NM-11 M 57 No No No No No pT1N0M0 I Right tongue
NM-13 F 40 No No Yes Yes No pT1N1M0 III Left tongue
M-11 M 71 Yes (-) No Yes Yes Yes pT4N2bM0 IV Right pyriform fossa
M-12 F 49 No No No Yes No T2N2bM0 IV Lower mandible alveolus
M-14 M 56 No No No No No pT3N1M0 III Right tongue
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Figure 1. Human papilloma virus (HPV) detection. PCR (left) for HPV detection using GP5/GP6 primers (expected product ~150bp). HPV in situ hybridization (right) using GenPoint in a representative HPV-negative HNSCC sample at a magnification of 40 x 10X; inset at magnification of 4 x 10X shows control HPV-positive nuclei stained brown.

Figure 1

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Summary of exome capture and sequencing results

Paired-end whole exome sequencing (WES) of all seven HNSCC samples and matched genomic DNA was performed on Illumina HiSeq 2000 platform. Each read was of 100 bp size. Additional details of the sequencing, including coverage and depth, are summarized in Table S1 (140.5KB, pdf) . Whole exome sequencing revealed a total of 3,959 single nucleotide variants across all 7 HNSCC samples, of which 2,547 are novel (Figure 2; Table 2, left panel). Nonsynonymous mutation rates ranged from 2.11 to 5.02 mutations per megabase (mean = 3.07) (Table 2, right panel). Several mutations recurred in more than one sample in both coding (Figure 3; Table 3) and non-coding regions (Table S2 (234.5KB, pdf) ). Nonsense and splice site variants were also identified in all samples (Table S3 (127.6KB, pdf) ).

Figure 2. Mutational landscape of HNSCC tumours. Left panel: Number of mutations (known and novel) in HNSCC patients Middle panel: significant somatic nucleotide variants (synonymous, nonsynonymous missense) Right panel: Rate of synonymous, nonsynonymous and other (3’ UTR, 3’ flank, 5’ UTR, 5’ flank, intron, splice site) mutations expressed in mutations per megabase of covered target sequence.

Figure 2

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Table 2. Number of somatic single nucleotide variants (SNVs) in HNSCC patients; total and (novel).

Sample ID NM-02 NM-08 NM-11 NM-13 M-11 M-12 M-14
Nonsynonymous
Missense 151 (106) 91 (55) 145 (111) 122 (90) 221 (61) 101 (67) 95 (65)
Nonsense 14 (11) 4 (4) 7 (6) 1 (1) 5 (4) 4 (4) 7 (5)
Synonymous 85 (49) 35 (14) 91 (61) 69 (35) 196 (30) 93 (45) 52 (20)
3’ UTR 199 (179) 131 (117) 176 (155) 156 (145) 477 (138) 206 (193) 200 (185)
3’ Flank 34 (32) 23 (20) 52 (49) 24 (23) 78 (25) 35 (31) 40 (37)
5’ UTR 22 (21) 14 (10) 15 (10) 14 (10) 32 (11) 17 (15) 17 (15)
5’ Flank 8 (4) 6 (5) 24 (18) 9 (8) 23 (8) 9 (6) 5 (5)
Intron 33 (32) 23 (17) 74 (56) 35 (33) 79 (20) 29 (26) 34 (30)
Splice site 4 (3) 2 (1) 2 (2) 2 (2) 1 (1) 3 (3) 3 (2)
Total (novel) 550 (437) 329 (243) 586 (468) 432 (347) 1112 (298) 497 (390) 453 (364)
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Figure 3. Somatic coding single nucleotide variants (SNV) found in ≥ 2 HNSCC patients and dbSNP database. The variant allele frequency (VAF) on the x-axis indicates the proportion of reads with the variant allele within individual samples.

Figure 3

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Table 3. Somatic coding single nucleotide variants (SNVs) found in ≥2 HNSCC patients. NS: nonsynonymous; S: synonymous. The variant allele frequency (VAF) indicates the proportion of reads with the variant allele within individual samples.

Gene Chr Position Base change Amino acid change Variant type Variant Allele Frequency (VAF) Freq COSMIC ID rsID
NM02 NM08 NM11 NM13 M11 M12 M14
CLMN chr14 95669509 A>G L726P NS 0.128 0.118 - 0.145 - 0.079 0.111 5/7 COSM1293528 -
CHEK2 chr22 29091840 T>C K152E NS 0.158 - - - 0.1 - 0.211 3/7 COSM42871 rs142470496
SFTPA1 chr10 81373600 G>A G160S NS 0.179 - - - 0.195 - - 2/7 - rs368889920
DRD5 chr4 9784542 A>C T297P NS - 0.429 - - - - 0.5 2/7 COSM1431796 rs2227851
NT5C3A chr7 33054388 T>C D283G NS 0.3 - - - - - 0.333 2/7 COSM222478 rs79747830
KRTAP13-3 chr21 31797833 C>T R133K NS - - 0.167 - - - 0.089 2/7 - -
PAK2 chr3 196509577 C>G Q101H NS - 0.8 - 0.086 - - - 2/7 COSM1422035 rs201465227
ST6GALNAC4 chr9 130674582 G>A - S 0.294 - - 0.1 0.222 0.286 0.436 5/7 - rs148599736
PPA1 chr10 71969413 A>G - S 0.118 0.143 - 0.109 0.108 - 0.16 5/7 - -
KRT83 chr12 52709871 G>A - S 0.173 - - 0.136 0.147 0.176 0.375 5/7 - -
MYLK chr3 123419183 G>A - S 0.104 0.17 - 0.122 - 0.067 0.064 5/7 - rs58176285
OR8I2 chr11 55861593 G>A - S 0.393 0.221 - 0.239 - 0.218 0.261 5/7 - -
HIST1H2BL chr6 27775319 G>A - S 0.078 - - 0.077 0.086 - 0.132 4/7 - rs141178835
ST6GALNAC4 chr9 130674558 C>T - S - 0.3 - 0.182 0.279 0.488 4/7 - -
PPA1 chr10 71969401 T>C - S 0.111 0.143 - 0.106 0.125 - - 4/7 - rs150430650
KRT83 chr12 52709724 A>G - S 0.101 0.097 - - 0.092 0.093 - 4/7 - -
KRT83 chr12 52709895 G>A - S 0.24 - - - 0.192 0.245 0.429 4/7 - -
OR1M1 chr19 9204157 T>C - S 0.129 - - 0.071 0.176 0.231 - 4/7 - -
OR1M1 chr19 9204184 G>A - S 0.325 - - 0.113 0.089 0.296 - 4/7 - -
HHIPL2 chr1 222715425 A>G - S 0.244 - - 0.17 - 0.17 0.111 4/7 - -
MYLK chr3 123419189 C>T - S 0.132 0.163 - 0.111 - - 0.065 4/7 - -
ASNS chr7 97498451 C>G - S 0.16 - - - 0.219 0.096 - 3/7 - rs76996735
IFITM1 chr11 315009 C>T - S 0.32 - - - 0.316 0.093 - 3/7 - rs3197137
KRT83 chr12 52709883 T>C - S - - - 0.161 0.167 - 0.375 3/7 - rs2248473
OR7D4 chr19 9324989 C>T - S 0.088 - - - 0.089 0.057 - 3/7 - rs111293642
OR7D4 chr19 9324995 C>T - S 0.068 - - - 0.072 0.05 - 3/7 - rs201732443
CHEK2 chr22 29091841 G>A - S 0.167 - - - 0.1 - 0.222 3/7 - rs146546850
OR10G7 chr11 123908827 T>C - S 0.17 - - 0.074 - 0.069 - 3/7 - -
KRT86 chr12 52699041 G>A - S - - - 0.141 - 0.127 0.114 3/7 - -
KRT86 chr12 52699545 G>A - S - - - 0.103 - 0.127 0.19 3/7 - rs374471358
KRT83 chr12 52710279 T>C - S 0.118 - - - - 0.137 0.267 3/7 - rs202206430
KRTAP4-8 chr17 39254154 C>T - S 0.167 - - 0.173 - 0.102 - 3/7 - -
DHX40 chr17 57663568 A>G - S - - 0.104 0.065 - - 0.062 3/7 - rs2697395
LCE1E chr1 152759892 A>T - S - 0.25 - - 0.263 - - 2/7 - -
FOLH1 chr11 49204790 A>G - S 0.292 - - - 0.139 - - 2/7 - rs76509850
KRT81 chr12 52681089 G>A - S - - - 0.167 0.214 - - 2/7 - -
KRT81 chr12 52681092 C>T - S - - - 0.167 0.214 - - 2/7 - -
KRT83 chr12 52710790 T>C - S 0.216 - - - - 0.25 - 2/7 - rs143202217
KRT83 chr12 52714757 T>C - S - - - 0.082 - 0.227 - 2/7 - -
KRT83 chr12 52710798 T>C - S 0.235 - - - - 0.268 - 2/7 - -
KRT83 chr12 52713122 C>T - S - - - 0.179 - 0.113 - 2/7 - -
SEH1L chr18 12955467 T>C - S - - - - 0.086 0.128 - 2/7 - -
KRTAP10-7 chr21 46020536 T>C - S 0.143 - - - 0.118 - - 2/7 - rs512211
KRTAP10-7 chr21 46020542 T>C - S 0.13 - - - 0.118 - - 2/7 - rs512214
HIST2H2AC chr1 149858563 C>T - S - - - - - 0.096 0.093 2/7 - -
HIST2H2AC chr1 149858593 C>T - S - - - - - 0.125 0.071 2/7 - -
KIAA1549 chr7 138601891 A>T - S 0.063 - - - - 0.098 - 2/7 - -
GIMAP5 chr7 150439323 A>G - S - - - - - 0.115 0.278 2/7 - -
KRTAP5-11 chr11 71293458 G>A - S - - - 0.093 - 0.095 - 2/7 - -
OR10G8 chr11 123901199 G>A - S - - - 0.118 - 0.074 - 2/7 - -
OR10G8 chr11 123901211 G>A - S - - - 0.136 - 0.12 - 2/7 - -
DUOX1 chr15 45433188 T>C - S 0.071 - - - - 0.081 - 2/7 - -
KRTAP4-11 chr17 39274373 G>A - S - - - - - 0.049 0.111 2/7 - -
KRTAP4-12 chr17 39280045 G>A - S - - - 0.14 - 0.145 - 2/7 - -
KRTAP10-4 chr21 45994676 A>G - S 0.103 - - - - 0.065 - 2/7 - -
HIST2H2AB chr1 149859383 C>T - S - - - 0.118 - - 0.071 2/7 - -
DRD5 chr4 9784550 G>A - S 0.375 - - - - - 0.5 2/7 - rs2227844
KRTAP5-5 chr11 1651760 C>T - S 0.11 - - - - - 0.077 2/7 - rs183750160
DPY19L2 chr12 63964600 G>A - S - - - 0.103 - - 0.105 2/7 - -
SETD8 chr12 123875311 C>T - S 0.385 - - 0.171 - - - 2/7 - rs74356260
POTEE chr2 132021452 C>A - S - 0.176 - 0.094 - - - 2/7 - -
CBWD1 chr9 163985 A>G - S - 0.065 0.062 - - - - 2/7 - -
ZNF814 chr19 58385762 C>G - S - - 0.263 0.353 - - - 2/7 - rs199732634
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Mutational landscape in HNSCC patients

On average, 227 coding mutations were identified per tumour, 39% of which are synonymous. The majority of the mutations identified were nonsynonymous missense mutations and mutations in the 3’ UTR region (Table 2). Filtering for driver and other significant variants using CHASM revealed alterations in genes that have been implicated in HNSCC or other cancers (Figure 2, middle panel; Table 4). Driver missense mutations in FGFR2 (Fibroblast Growth Factor Receptor 2), SETBP1 (SET Binding Protein 1), PIK3CA (Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha), IGF2BP3 (Insulin Like Growth Factor 2 MRNA Binding Protein 3), TP53 (Tumour Protein P53), PTPN11 (Protein Tyrosine Phosphatase, Non-Receptor Type 11) and NF2 (Neurofibromin 2) were identified. Significant missense mutations were also identified in ASNS (Asparagine Synthetase (Glutamine-Hydrolyzing)) in four of the seven samples. Other genes that exhibited recurrent mutations included the CLMN (Calmin) gene (5/7), CHEK2 (Checkpoint Kinase 2) (3/7), and DRD5 (Dopamine Receptor D5) and PAK2 (P21 (RAC1) Activated Kinase 2) (2/7) (Table 3). These recurrent mutation sites have not been reported as hotspots in previous HNSCC sequencing studies.

Table 4. Somatic single nucleotide variants (SNVs) in HNSCC patients in coding regions. NS MS: nonsynonymous missense; S: synonymous. Driver missense variants are in bold text and synonymous variants in possible driver genes are marked with an asterisk (*).The variant allele frequency (VAF) indicates the proportion of reads with the variant allele within individual samples. The minor allele frequency (MAF) signifies prevalence of the known variants in the global population as per the ExAc dataset.

Sample ID Gene Chr Position Variant type Base change Amino acid change Variant allele frequency Minor allele frequency rsID COSMIC ID
NM-02 FGFR2 chr10 123256128 NS MS G>T P595H 0.273 - - -
SETBP1 chr18 42530740 NS MS G>T G479C 0.13 - - -
ASNS chr7 97498395 NS MS G>A A25V 0.225 - - -
chr7 97498404 NS MS A>G M22T 0.243 - - -
KIF21B chr1 200954042 NS MS G-T R1250S 0.143 - - -
UBA7 chr3 49848502 NS MS G>T P382H 0.132 - - -
KDM3B chr5 137735569 NS MS G>T A1023S 0.158 - - -
EXOSC1 chr10 99196233 NS MS G>T A186D 0.3 - - -
DENND5A chr11 9166573 NS MS C>A V1031F 0.273 - - -
DGKZ chr11 46394214 NS MS G>T G541V 0.5 - -
FOLH1 chr11 49186320 NS MS G>C N459K 0.227 0.00003 rs201724751 -
chr11 49204779 NS MS C>T R281H 0.3 0.0351 rs116795343 -
FAT3 chr11 92087697 NS MS G>T G807C 0.211 - - -
SLC7A7 chr14 23282391 NS MS G>T L73M 1 - - -
CEP128 chr14 81244269 NS MS A>T L778Q 0.174 - - -
EML2 chr19 46130008 NS MS C>A W433C 0.3 - - -
CHRNA4 chr20 61981122 NS MS C>A K547N 0.375 - - -
GART chr21 34889834 NS MS C>T R595Q 0.2 0.0003 rs202015633 -
CHEK2 chr22 29091840 NS MS T>C K416E 0.158 0.0259 rs74751600 -
ARID2* chr12 46245344 S G>T S1146S 0.333 - - -
NM-08 ASNS chr7 97498378 NS MS C>T A31T 0.167 - - -
ZFHX4 chr8 77618158 NS MS G>T G612V 0.231 - - COSM73358
CKAP5 chr11 46819413 NS MS C>G C427S 0.12 - - -
SF1 chr11 64537028 NS MS C>A R303L 0.097 - - -
HECTD4 chr12 112669460 NS MS C>G K1885N 0.158 - - -
FBN1 chr15 48744840 NS MS C>T A1822T 0.273 0.00003 rs777539060 -
HELZ chr17 65144830 NS MS G>T L826I 0.2 - - -
NM-11 RALGPS2 chr1 178855145 NS MS C>T T361M 0.125 - - -
DYNC1I2 chr2 172584439 NS MS C>A P369T 0.125 - - -
NFE2L2 chr2 178098966 NS MS C>A D27Y 0.188 - - -
POSTN chr13 38154051 NS MS G>T P536Q 0.111 - - -
INO80 chr15 41377611 NS MS G>A R277C 0.158 - - -
CDH16 chr16 66949240 NS MS G>T P156T 0.364 - - -
PRPSAP2 chr17 18785908 NS MS T>C L147S 0.098 - - -
NM-13 ASNS chr7 97498378 NS MS C>T A31T 0.125 - - -
ASNS chr7 97498395 NS MS G>A A25V 0.105 - - -
GIGYF2 chr2 233684687 NS MS C>T R862C 0.138 0.00002 rs561616045 -
CBLB chr3 105464767 NS MS G>T P280H 0.097 - - -
LAP3 chr4 17598708 NS MS C>A A343D 0.214 - - -
TRIM7 chr5 180625732 NS MS G>A L316F 0.156 - - -
ABCB8 chr7 150733032 NS MS G>A A331T 0.227 0.00004 rs777741819 -
ESRP1 chr8 95674755 NS MS G>C V206L 0.079 - - -
ADCY6 chr12 49176793 NS MS C>A R142L 0.375 - - -
NFATC4 chr14 24843541 NS MS C>T S581L 0.25 - - COSM3793625
EML5 chr14 89124732 NS MS C>A G1226W 0.143 - - -
ANKFY1 chr17 4086708 NS MS G>T A688E 0.176 - - -
UQCRFS1 chr19 29698630 NS MS C>A C217F 0.25 - - -
ITSN1 chr21 35237479 NS MS G>T M1305I 0.667 - - -
ABCB7 chrX 74332770 NS MS C>G C96S 0.111 - - -
HDX chrX 83730396 NS MS G>C R4G 0.231 - - -
M-11 PIK3CA chr3 178936091 NS MS G>A E545K 0.278 0.000008 rs104886003 COSM763
IGF2BP3 chr7 23353160 NS MS A>G I503T 0.211 0.0040 rs79900450 -
TP53 chr17 7577106 NS MS G>C P278A 0.647 - - COSM10814
SLC8A1 chr2 40656504 NS MS C>T G306D 0.234 - - -
MITF chr3 70008494 NS MS C>A Q362K 0.333 - - -
VEPH1 chr3 157034861 NS MS A>G L622P 0.139 - - -
chr3 157099046 NS MS C>G L342F 0.208 - - -
GNGT1 chr7 93536114 NS MS T>C V19A 0.133 - - -
ARHGEF10 chr8 1824752 NS MS A>G D232G 0.214 - - -
NEBL chr10 21098782 NS MS T>A D855V 0.339 - - -
NAALAD2 chr11 89891404 NS MS A>C L296F 0.375 - - -
SMG8 chr17 57290439 NS MS A>T H752L 0.25 - -
RBM39 chr20 34302295 NS MS C>A C303F 0.15 - - -
M-12 ASNS chr7 97498378 NS MS C>T A31T 0.214 - - -
GRK7 chr3 141499490 NS MS A>C Y296S 0.273 - - -
TIPARP chr3 156413805 NS MS C>A P413Q 0.121 - - -
RGS3 chr9 116346401 NS MS C>A S903R 1 - - -
SPTBN2 chr11 66472616 NS MS C>A G711C 1 - - -
UBE4A chr11 118253450 NS MS C>A A726E 0.15 - - -
TP53 chr17 7577538 NS MS C>T R248Q 0.286 0.00006 rs11540652 COSM10662
CDC27 chr17 45229257 NS MS T>C T335A 0.167 0.00002 rs199890121 -
HELZ chr17 65163619 NS MS C>A C575F 0.667 - - -
ALK* chr2 29474099 S C>A G692G 1 - - -
M-14 PTPN11 chr12 112892407 NS MS T>G S189A 0.167 0.0027 rs79068130 -
NF2 chr22 30090766 NS MS G>T R588L 1 - - -
MLL3* chr7 151962176 S T>A P377P 0.084 0.4554 rs62478356 COSM4162022
MYC* chr8 128750817 S C>A T118T 0.5 - - -
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Synonymous variants in previously identified driver genes ARID2 (AT-Rich Interaction Domain 2), ALK (Anaplastic Lymphoma Receptor Tyrosine Kinase), MLL3 [Myeloid/Lymphoid Or Mixed-Lineage Leukemia 3, also known as KMT2C (Lysine Methyltransferase 2C)] and MYC (V-Myc Avian Myelocytomatosis Viral Oncogene Homolog), were also identified (Figure 2, middle panel; Table 4). The ASNS gene was found to have a synonymous mutation in three samples, and recurrent synonymous mutations were also observed in CHEK2 and DRD5 genes (Table 3). Splice site variants in FCGR2A (Fc Fragment of IgG, Low Affinity IIa, Receptor (CD32)) and two genes involved in eukaryotic translation initiation [EIF4B (Eukaryotic Translation Initiation Factor 4B) and EIF4A3 (Eukaryotic Translation Initiation Factor 4A3)] were seen in two of the seven samples (Table S3 (127.6KB, pdf) ). Significant non-coding mutations were filtered using CADD (Table S4 (112KB, pdf) ). In the 3’UTR region, mutations in IGF1R (Insulin Like Growth Factor 1 Receptor) and ERBB4 (Erb-B2 Receptor Tyrosine Kinase 4) were identified as significant. Another eukaryotic translation initiation factor, EIF2B4 (Eukaryotic Translation Initiation Factor 2B Subunit Delta), exhibited significant splice site variance. IntOGen pathway analysis revealed that the MAP kinase pathway was the most significantly affected pathway in all samples tested. In addition, cell cycle, actin cytoskeleton regulation, PI3K-Akt signaling and other pathways in cancer were among those significantly enriched for exomic alterations in all samples (Table 5). Genes with driver mutations implicated in multiple pathways included FGFR2, PIK3CA, and TP53. Significant mutations in the pathway genes were all deleterious with respect to protein function as predicted by SIFT and PolyPhen.

Table 5. Significantly involved pathways (p ≤ 0.05) identified by IntOGen-Mutations platform. Driver mutations in each pathway are in bold text and marked with an asterisk (*).

Pathway ID KEGG annotation Total genes in pathway Number of genes affected Pathway genes with significant/ driver (*) mutations
hsa04010 MAPK signaling pathway 257 46 FGFR2*
PIK3CA*
TP53*
hsa04110 Cell cycle 124 35 TP53*
CHEK2
CDC27
hsa05166 HTLV-1 infection 260 60 PIK3CA*
TP53*
CHEK2
CDC27
ADCY6
NFATC4
hsa05200 Pathways in cancer 326 71 FGFR2*
PIK3CA*
TP53*
CBLB
ADCY6
ADCY6
GNGT1
MITF
hsa04810 Regulation of actin cytoskeleton 213 46 FGFR2*
PIK3CA*
hsa04151 PI3K-Akt signaling pathway 338 80 FGFR2
PIK3CA*
TP53*
GNGT1
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Asparagine synthetase protein modeling

The ASNS gene codes for asparagine synthetase, which catalyzes the formation of asparagine from glutamine, aspartate and ATP. Protein modeling of the effect of the three novel, recurrent mutations in ASNS identified in this cohort revealed that the mutated amino acids (p.A13T, p.A25V and p.M22T) are located in the vicinity (within 10 Å distance) of the glutamine binding pocket (Figure 4).

Figure 4. Homology model of the N-terminal domain of human asparagine synthetase (ASNS) complexed with glutamine (Gln). Amino acid changes due to nonsynonymous mutations in ASNS are indicated.

Figure 4

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Discussion

This is the first study reported in the literature to describe the mutational landscape of Pakistani HNSCC patients. We performed exome sequencing of a small set of HPV-negative HNSCC patients from Pakistan. We identified a total of ~4000 somatic variants (novel and known). Previous studies have reported greater number of mutations in HPV-negative as compared to HPV-positive HNSCC tumours (Riaz et al., 2014; Beck and Golemis, 2016). As a comparison, Stransky et al. (2011) on average found 130 coding mutations per tumour (25% synonymous), while in the current cohort an average of 227 coding mutations per tumour (39% synonymous) were identified.

Several variants were found in more than one sample and in genes that have been previously identified to play a role in HNSCC carcinogenesis. Next generation sequencing studies in other populations have identified mutations in the tumour suppressor gene TP53, which is associated with smoking-related disease, and the oncogene PIK3CA, at a mutation rate of 40-60% and 6-8%, respectively (Agrawal et al., 2011; Stransky et al., 2011; Loyo et al., 2013). The TCGA study, with the largest cohort to date, reported a TP53 mutation rate of 72% and PIK3CA mutation rate of 18-21% (TCGA 2015). Mutations in TP53 gene were detected in two of the seven cases in the current study, and in PIK3CA in one patient. In a comparative genomic analysis of HPV-positive and HPV-negative tumours, the former showed mutations in FGFR2 and MLL3, among others. The mutational spectrum in HPV-negative tumours closely resembled lung and esophageal squamous cell carcinomas, with mutations identified in genes including TP53, MLL2/3, NOTCH1, PIK3CA and DDR2 (Seiwert et al., 2015). The HPV-negative cohort in the current study exhibited a nonsense variant (p.Y223X) in DDR2 in a single sample. A different nonsense mutation (p.R709X) and missense mutations (p.I474M; p.I724M) have been previously identified exclusively in HNSCC recurrences (Hedberg et al., 2015). DDR2 and FGFR2, which was identified as having a potential missense driver mutation in one sample in the current study, are both genes that code for receptor tyrosine kinases and are potentially targetable for therapeutics. In addition, an SNV was identified in MLL3 in a sample that also exhibited an SNV in the driver gene MYC. MLL genes encode histone lysine methyltransferases that are involved in chromatin remodeling. Recurrent mutations in MLL genes have been identified in several other cancers, including lung squamous cell carcinoma, and been associated with poor clinical outcomes (Morin et al., 2011; Grasso et al., 2012; Jones et al., 2012; Kim et al., 2014; Seiwert et al., 2015). The oncogene MYC is most often altered in HPV-negative HNSCC tumours (TCGA 2015).

Additionally, we discovered recurrent significant missense mutations in ASNS (asparagine synthetase) gene in 4 out of 7 samples. These SNVs in ASNS have not previously been reported in the literature as significant in HNSCC pathogenesis. The ASNS gene codes for a ubiquitously expressed, ATP-dependent enzyme that converts aspartate and glutamine to asparagine and glutamate (Balasubramanian et al., 2013). The protein folds into two distinct domains, where the N-terminal domain contains two layers of antiparallel beta-sheets. The active site responsible for the binding and hydrolysis of glutamine is situated between these layers and important, evolutionarily conserved side chains involved in glutamine binding within the substrate binding pocket include Arg 49, Asn 74, Glu 76, and Asp 98 (Van Heeke and Schuster, 1989). While the amino acids mutated as a result of the novel and recurrent mutations in ASNS identified in this cohort are not part of the glutamine binding pocket, protein modeling revealed their proximity to the region. Therefore, these mutations may affect glutamine binding during catalysis. Elevated levels of ASNS play a role in drug resistance in acute lymphoblastic leukemias and have been implicated in solid tumour adaptation to nutrient deprivation and hypoxia (Balasubramanian et al., 2013). ASNS expression has also been shown to be an independent factor affecting survival in hepatocellular carcinoma and low ASNS levels are correlated with poorer surgical outcomes (Zhang et al., 2013). In HNSCC, deregulation of miR-183-5p and its target gene ASNS has been documented in a radiochemotherapy cell culture model of primary HNSCC cells and is a potential prognostic marker for radiochemotherapy outcome (Summerer et al., 2015). Two recent reports have further elucidated the role of ASNS in carcinogenesis. One showed that ASNS expression in primary tumours is correlated with metastatic relapse and bioavailability of asparagine regulates metastatic potential and progression in breast cancer cells, potentially by affecting the epithelial-to-mesenchymal transition (Knott et al., 2018). ASNS was also identified as a key target of the KRAS-ATF4 axis in non-small-cell lung cancer. Oncogenic KRAS regulates amino acid homeostasis and cellular response to nutrient stress via the ATF4 target ASNS, which subsequently contributes to inhibition of apoptosis and increase in proliferation of cancer cells (Gwinn et al., 2018). While KRAS mutations are uncommon in HNSCC, particularly as compared to HRAS (Rothenberg and Ellisen, 2012), mutations in ASNS could effectively have the same functional consequences. Given the role of ASNS in cellular stress and the unfolded protein response, it is an intriguing target for further study in HNSCC pathogenesis.

The current analysis also revealed significant low-frequency driver mutations in SETBP1, IGF2BP3, PTPN11 and NF2. SETBP1 was identified in a patient who also had a driver mutation in FGFR2. SETBP1 encodes a nuclear protein and its overexpression results in inhibition of the tumour-suppressor PP2A serine-threonine phosphatase activity (Cristobal et al., 2010). Mutations in SETBP1 resulting in overexpression or gain of function have been documented previously in hematological malignancies (Ciccone et al., 2015).

An IGF2BP3 mutation was found in a sample that also had driver mutations in PIK3CA and TP53. The protein product of IGF2BP3 is an RNA-binding factor that promotes cancer invasion by binding to transcripts that encode proteins, such as CD44, for functions related to cell migration, proliferation and adhesion (Ennajdaoui et al., 2016). IGF2BP3 mutations and copy number variations have been reported previously in HNSCC (Lin et al., 2011; Clauditz et al., 2013; Jimenez et al., 2015), and its role in cell invasiveness and metastasis in several other cancers has been documented in the literature (Schaeffer et al., 2010; Lin et al., 2011; Taniuchi et al., 2014; Hsu et al., 2015; Shantha Kumara et al., 2015; Belharazem et al., 2016; de Lint et al., 2016; Ennajdaoui et al., 2016).

Mutations in PTPN11 and NF2 genes were found in the same sample. The protein encoded by the proto-oncogene PTPN11 is a cytoplasmic tyrosine phosphatase, which is widely expressed in most tissues and known to play a regulatory role in normal hematopoiesis, and in mitogenic activation, metabolic control, transcription regulation, and cell migration signaling pathways (Chan and Feng, 2007). Somatic PTPN11 mutations have been detected in juvenile myelomonocytic leukemia, myelodysplastic syndromes and acute myeloid leukemia (Tartaglia et al., 2003; Chan and Feng, 2007). While PTPN11 mutations have not been reported previously in HNSCC, this gene has been identified as a target of the tumour-suppressive microRNA miR-489. Knockdown of PTPN11 in HNSCC cell lines resulted in the inhibition of cell proliferation (Kikkawa et al., 2010). Neurofibromatosis type 2 (NF2) is a tumour suppressor gene on chromosome 22q12 that encodes for merlin, a membrane-cytoskeleton scaffolding protein that inhibits key signaling pathways crucial to cell proliferation, such as the PI3K pathway. Somatic NF2 mutations have been reported in a number of different cancers (Schroeder et al., 2014). In HNSCC, chromosome 22q is a frequent site of allele loss. Merlin and the cytoplasmic tail of CD44, which is regulated at the transcript level by IGF2BP3 gene product as mentioned above, create a molecular switch complex that is responsible for either cell growth or proliferation (Morrison et al., 2001).

In addition to non-synonymous mutations, synonymous mutations are known to frequently act as driver mutations in cancers (Supek et al., 2014). We identified SNVs in MLL3, ARID2 and ALK. Mutations in MLL and ARID gene families have been previously documented for HNSCC (India Project Team of the International Cancer Genome Consortium, 2013; Martin et al., 2014). The ALK gene encodes yet another receptor tyrosine kinase, which has been found to be aberrantly expressed in several tumours, including anaplastic large cell lymphomas (Chiarle et al., 2008; Salaverria et al., 2008), neuroblastoma (Lasorsa et al., 2016; Theruvath et al., 2016; Ueda et al., 2016) and non-small cell lung cancer (Soda et al., 2007; Quere et al., 2016).

A study of gingivo-buccal oral squamous cell carcinoma (OSCC-GB), an HNSCC clinical sub-type, in the Indian population revealed frequently altered genes that are specific to OSCC-GB and others that are also affected in HNSCC (India Project Team of the International Cancer Genome Consortium, 2013). Altered genes that are common between the OSCC-GB study and the current study in the Pakistani population are ARID2 and TP53. MLL family member MLL4 was also identified as a frequently altered gene specific to OSCC-GB. Other genes identified in the study in the Indian population, such as CASP8, HRAS and NOTCH1, are also altered in HNSCC in other populations (albeit at different frequencies and with varying significance) (Agrawal et al., 2011; Stransky et al., 2011; Seiwert et al., 2015; The Cancer Genome Atylas Network, 2015; Al-Hebshi et al., 2016), but were not identified in this study.

The small sample size is a limitation of this study, which may explain low frequency of commonly mutated genes and why some of the commonly occurring HNSCC mutations such as NOTCH1 and HRAS were not identified in this small cohort. However, given limited resources, it was deemed important to establish preliminary data prior to a larger scale study. The approach of using a smaller discovery cohort followed by validation of identified mutations in a larger cohort has been proposed and taken by others and reported in the literature (Bacchetti et al., 2011; Nichols et al., 2012; Romero Arenas et al., 2014; Hedberg et al., 2015). It is also possible that given the heterogeneous nature of this disease and unique set of risk factors compared to Western countries, the predominant driver gene mutations may vary among populations. Previous studies in East and South Asian populations with oral squamous cell carcinoma have highlighted that the pattern of genetic mutations is significantly different from tumour profiles in other studies largely conducted in Caucasian populations (Vettore et al., 2015; Su et al., 2017). Population-based differences in mutational profile have also been documented for other cancer types. In lung cancers, several studies have highlighted the geographic variations in genes such as EGFR and LKBI between Asian (Chinese, Japanese, Korean) and Caucasian populations (Koivunen et al., 2008; Mitsudomi, 2014; Li et al., 2015).

This is the first report describing the mutational spectrum of Pakistani HNSCC patients. In addition to reporting known HNSCC mutations, we have identified novel, recurrent mutations in ASNS and other genes in the Pakistani population. It has been well established that a complex interplay of genetic and environmental factors results in varying risk of cancer development and treatment outcomes across different ethnicities and geographic regions (Ma et al., 2010). Such diversity among different populations can be explained by the type and frequency of variations in both germline and somatic genomes (Wang and Wheeler, 2014). Therefore, this study is an important step towards gaining a better mechanistic understanding of the complex nature of HNSCC. Future studies will be undertaken to confirm and validate the findings from this study in a larger cohort. Additionally, functional analysis of mutations and correlation with clinical outcomes will be performed.

Acknowledgments

This work was supported by the Higher Education Commission of Pakistan (20-1224-R&D/2009 to K.G. and M.J.K). The funding source had no involvement in the study design and conduct or preparation of the article. The authors gratefully acknowledge Aisha Nazir for her role in pre-sequencing sample processing, Muhammed Murtaza and Faiz Gani for their input and support in the initial stages of this project, and Faizan Saleem for his help with data analysis. HPV primers (GP5/GP6) were graciously provided by Dr SH Ali (then at Aga Khan University, Pakistan).

Supplementary material

The following online material is available for this article

Figure S1. HNSCC samples.
Click here for additional data file. (492.5KB, pdf)
Table S1. Whole exome sequencing data summary.
Click here for additional data file. (140.5KB, pdf)
Table S2. Somatic non-coding single nucleotide variants (SNVs) found in ≥ 2 HNSCC patients.
Click here for additional data file. (234.5KB, pdf)
Table S3. Genes with somatic mutations in HNSCC patients resulting in nonsense or splice site variants.
Click here for additional data file. (127.6KB, pdf)
Table S4. Significant single nucleotide variant (SNV) mutations in HNSCC patients in non-coding regions.
Click here for additional data file. (112KB, pdf)

Associate Editor: Ricardo G. Correa

Conflict of Interest

The authors have no conflicts to declare.

Author contributions

KG was involved in conceiving and designing the study, data analysis and interpretation, and drafted the manuscript; SSR conceived and designed the study, processed the samples prior to sequencing, analyzed and interpreted the data and contributed in writing the manuscript; SAR and MKA were involved in data analysis and interpretation, and contributed to the manuscript; SM contributed to data acquisition and manuscript writing; RA performed the histopathological examination of HNSCC samples and contributed to the manuscript; MJK was involved in conceiving and designing the study and was responsible for sample resection and acquisition. All authors read and approved the final version of the manuscript.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Figure S1. HNSCC samples.
Click here for additional data file. (492.5KB, pdf)
Table S1. Whole exome sequencing data summary.
Click here for additional data file. (140.5KB, pdf)
Table S2. Somatic non-coding single nucleotide variants (SNVs) found in ≥ 2 HNSCC patients.
Click here for additional data file. (234.5KB, pdf)
Table S3. Genes with somatic mutations in HNSCC patients resulting in nonsense or splice site variants.
Click here for additional data file. (127.6KB, pdf)
Table S4. Significant single nucleotide variant (SNV) mutations in HNSCC patients in non-coding regions.
Click here for additional data file. (112KB, pdf)

Data Availability Statement

The data sets supporting the results of this article are included within the article and its supplementary files. The raw sequencing data of those patients that consented to deposition of data in a public database (4 out of 7 total) have been deposited in NCBI’s Sequence Read Archive and are accessible through accession number SRP083063.

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