Abstract
A cohort study of 292 Chinese women was conducted to determine the relationship between human papillomavirus (HPV) type 16 variants and persistent viral infection. Enrolled patients were HPV16 positive and had both normal cytology and histology. Flow-through hybridization and gene chip technology was used to identify the HPV type. A PCR sequencing assay was performed to find HPV16 E2, E6 and E7 gene variants. The associations between these variants and HPV16 persistent infection was analyzed by Fisher’s exact test. It was found that the variants T178G, T350G and A442C in the E6 gene, as well as C3158A and G3248A variants in the E2 gene were associated with persistent HPV16 infection. No link was observed between E7 variants and persistent viral infection. Our findings suggest that detection of specific HPV variants would help identify patients who are at high risk for viral persistence and development of cervical neoplasia.
Keywords: Human papillomavirus, persistent infection, variants
Introduction
It is well known that persistent infection with high risk human papillomavirus (HPV) is the primary cause of cervical cancer, especially type 16 [1-3]. To date, about one hundred HPV types have been identified and characterized. For a given HPV type, viral isolates that differ by less than 2% of their DNA sequence for the L1 gene are defined as variants [4]. The sequencing analysis revealed the existence of numerous natural variants that differ from the original prototype sequence by up to 2% in the coding region and up to 5% in the noncoding region. Therefore, HPV16 variants were divided into five major phylogenetic clusters: Asian, Asian American, North American, European and African [5]. Multiple studies have documented that HPV16 E6 variants contribute to persistent viral infection and the development of cervical neoplasia [6-15].
Persistent infection plays a key role in the development of cervical cancer; therefore, prediction of persistent HPV16 infection is an important step for cervical cancer prevention. To our knowledge, there is no study exploring the association between persistent HPV16 infection and variants within the Chinese Han population. The purpose of this study was to determine the distribution of HPV16 variants among women who live in Shanghai, China. We collected exfoliated cervical cells and sequenced the HPV16 DNA, in order to detect HPV16 variants associated with persistent infection.
Materials and methods
Subject recruitment and sample collection
Patients who came to the gynecologic clinic at the People’s Hospital of Shanghai Pudong District between May 2011 and October 2012 for cervical disease were enrolled in this study. Patients were excluded from this study for the following reasons: 1) confirmed cervical intraepithelial neoplasia (CIN), cervical cancer or other malignancies, 2) previous therapeutic procedure to cervix, 3) pregnancy. In order to be eligible for this study patients had to meet the following criteria: 1) positive for only HPV16, confirmed by flow-through hybridization and gene chip technology, 2) no histologic abnormality on cytology or biopsy, 3) be between the ages of 30 and 70 years and have lived in Shanghai for at least 2 years, 4) be of Chinese Han ethnicity. The infectious profile of enrolled participants with HPV16 infection was detected at one year intervals. All participants provided written, informed consent. The study was approved by the Ethics Committee of the Hospital and conducted in accordance with the 2008 Declaration of Helsinki.
Molecular HPV16 variant analysis
An aliquot of 5 µl from each sample was amplified for β-globin DNA. Specimens that were positive for both β-globin and HPV16 were used to amplify E2, E6 and E7 genes with specific primers. Briefly, the template (5 µl) was used in a 100 µl reaction volume with ampliTag Gold DNA polymerase for PCR. The PCR primers are listed in Table 1. Amplification was carried out for 36 cycles. The PCR products were purified with the QIAquick gel extraction kit (Qiagen). PCR sequencing was performed by the fluorescent cycle-sequencing method (BigDye terminator ready-reaction kit; Perkin-Elmer) on an ABI Prism 3100 Genetic Analyzer system. The variations were confirmed by a second PCR sequencing.
Table 1.
Primers used to amplify the target genes
| Name | Sequence | Annealing Tempreture (°C) | Product length (bp) |
|---|---|---|---|
| HPV16 E6 | F: 5’ TATAAAACTAAGGGCGTAAC 3’ | ||
| R: 5’ CATGCAATGTAGGTGTATCT 3’ | 48 | 573 | |
| HPV16 E2 | F: 5’ CGGAAATCCAGTGTATGAGC 3’ | ||
| R: 5’ AAAGCACGCCAGTAATGTTG 3’ | 56 | 1240 | |
| HPV16 E7 | F: 5’ TTGCAGATCATCAAGAACAC 3’ | ||
| R: 5’ TACAGCCTCTACATAAAACC 3’ | 50 | 417 |
Statistical analysis
Patients with isolated HPV16 infection were considered to have a persistent infection if they had the same HPV type infection after one year. SPSS software (Version 18.0; SPSS Inc, Chicago, IL) was used for this study. The association between persistent HPV16 infections and variants was assessed by Fisher’s exact test. P-values less than 0.05 were considered statistically significant.
Results
A total of 32,686 women were enrolled in this study and underwent flow-through hybridization and gene chip assay. 3,363 women came back positive for an isolated HPV16. Among the HPV16 positive women, 3,063 cases were further excluded due to aberrant cytological and pathological morphology. An additional eight cases were excluded due to target gene amplification failure. A total of 292 women underwent PCR amplification and sequencing analysis for this study (Figure 1).
Figure 1.
Test results and outcome. A total of 32,686 women were enrolled in this study and underwent flow-through hybridization and gene chip assay. 3,363 women came back positive for an isolated HPV16. Among the HPV16 positive women, 3,063 cases were further excluded due to aberrant cytological and pathological morphology. An additional eight cases were excluded due to target gene amplification failure. A total of 292 women underwent PCR amplification and sequencing analysis for this study.
199 of the 292 study participants (68.15%) had the E6 HPV16 T178G Asia prototype variant (As.P). Of the remaining participants 4.79% had the European prototype (EP), 9.25% Asian variants, 15.07% European variants, and 2.75% had the Africa 1 variant (Af1). As for European variants, we detected both T350G and A442C at the same time. Further analysis demonstrated that both the Asian variant of E6 T178G and the European variant of E6 T350G and A442C were associated with HPV16 persistent infection (P=0.007 and P<0.001 respectively; Table 2).
Table 2.
Variants among HPV16 E2, E6 and E7 genes
| Nucleotide substitutions | Predicted amino acid substitution | N | Percentage (%) | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
|
|||||||||||||||||||||||
| E6 | E7 | E2 | E6 | E7 | E2 | |||||||||||||||||||
| Variant classes | 1 | 1 | 1 | 3 | 3 | 4 | 6 | 6 | 8 | 2 | 2 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | |||||
| 3 | 7 | 7 | 3 | 5 | 4 | 4 | 4 | 4 | 8 | 9 | 1 | 2 | 3 | 4 | 4 | 5 | 6 | 7 | ||||||
| 1 | 6 | 8 | 5 | 0 | 2 | 6 | 7 | 6 | 2 | 2 | 5 | 4 | 8 | 0 | 4 | 2 | 8 | 8 | ||||||
| 7 | 5 | 8 | 8 | 3 | 9 | 8 | 3 | 3 | 6 | |||||||||||||||
| HPV16-R(E-P) | A | G | T | C | T | A | A | A | T | G | A | C | G | T | C | G | T | C | C | |||||
| E-P | - | - | - | - | - | - | C | - | G | - | - | - | - | - | - | - | - | - | N29H | - | 14 | 4.79 | ||
| As-A131C | c | - | A | - | - | - | C | a | G | - | - | - | - | - | - | - | A | -/D25E | N29H | -/-/D344E | 27 | 9.25 | ||
| E-G176A | - | A | - | - | - | - | - | G | - | - | - | - | - | - | - | - | D25N | - | - | 14 | 4.79 | |||
| As-T178G | - | - | G | - | - | - | G | c | - | G | - | - | - | T | - | - | A | - | D25E | N29S/- | -/P219S/T310K | 75 | 25.68 | |
| Af1-C335T | - | - | - | T | - | - | - | G | - | - | - | - | - | - | - | - | H78Y | - | - | 8 | 2.75 | |||
| E-T350G | - | - | - | - | G | C | - | G | - | - | - | - | - | - | - | - | L83V/E113D | - | - | 30 | 10.27 | |||
| As | - | - | G | - | - | - | a | G | A | A | - | - | - | - | - | A | D25E | - | -/-/T135K/R165Q/D344E | 73 | 25.00 | |||
| As | - | - | G | - | - | - | G | c | - | G | - | - | C | - | A | c | - | - | D25E | N29S/- | -/I210T/E232K/- | 50 | 17.13 | |
| As | - | - | - | - | - | - | G | G | - | - | C | - | A | c | - | - | D25E | N29S | -/I210T/E232K/- | 1 | 0.34 | |||
Six variants were found in the E6 gene of HPV16, including G176A, T178G, C335T, T350G, A442C and A131C. Among these variants, A131C is a silent mutation, the remainder of the variants resulted in missense mutations (Table 3). 189 of the 292 total cases were identified as transient HPV16 infections, while 103 cases were confirmed as persistent HPV16 infections (Table 3). The T178G (P=0.007), T350G (P<0.001) and A442C (P<0.001) variants in E6 were found to be associated with persistent infection. In the E7 gene, three variants were identified, including A646C, A647G, and T846C. However, there was no link between the variants and persistent HPV 16 infection (Table 4). As for the E2 gene, 43 cases had an E2 deletion. Among the other 249 cases, seven missense mutation and two silent mutation variants were identified. Further analysis demonstrated that among the E2 variants the C3158A (P<0.035) and G3248A (P<0.035) were associated with persistent HPV16 infection (Table 5).
Table 3.
Relationship between E6 variants and HPV16 persistent infection
| Nucleotide sequence variation | Amino acide variation | Infection | P | |
|---|---|---|---|---|
|
|
||||
| Transient (n=189) | Persistent (n=103) | |||
| A131C | R10R | 10 (5.29) | 17 (16.50) | ˉ |
| G176A | D25N | 6 (3.17) | 8 (7.77) | 0.091 |
| T178G | D25E | 139 (73.54) | 60 (58.25) | 0.007* |
| C335T | H78Y | 3 (1.59) | 5 (4.85) | 0.135 |
| T350G | L83V | 4 (2.15) | 26 (25.24) | <0.001* |
| A442C | E113D | 4 (2.15) | 26 (25.24) | <0.001* |
Fisher exact test.
p<0.05, E6 variants associate with HPV16 persistent infection.
Table 4.
Relationship between E7 variants and HPV16 persistent infection
| Nucleotide sequence variation | Amino acide variation | Infection | P | |
|---|---|---|---|---|
|
|
||||
| Transient (n=189) | Persistent (n=103) | |||
| A646C | N29H | 24 (12.70) | 17 (16.50) | 0.085 |
| A647G | N29S | 67 (35.45) | 59 (57.28) | 0.074 |
| T846C | S95S | 98 (51.85) | 27 (26.21) | ˉ |
Fisher exact test.
Table 5.
Relationship between E2 variants and HPV16 persistent infection
| Nucleotide sequence variation | Amino acid variation | Infection | P | |
|---|---|---|---|---|
|
|
||||
| Transient (n=155) | Persistent (n=94) | |||
| G2827A | D25D | 27 | 22 | 0.254 |
| C3158A | T135K | 28 | 8 | 0.035* |
| G3248A | R165Q | 28 | 8 | 0.035* |
| T3383C | I210T | 14 | 11 | 0.504 |
| C3409T | P219S | 23 | 15 | 0.824 |
| G3448A | E232K | 14 | 12 | 0.356 |
| T3523C | L257L | 14 | 12 | 0.356 |
| C3683A | T310K | 14 | 11 | 0.504 |
| C3786A | D344E | 26 | 10 | 0.175 |
Fisher exact test.
p<0.05, E2 variants associate with HPV16 persistent infection.
Discussion
Cervical cancer is the third most common gynecologic neoplasm, with the highest incidence seen in less developed countries. The incidence is primarily influenced by human papillomavirus (HPV) infection. Persistent infection with high risk human papillomavirus is a key factor in the development of cervical cancer. High risk HPV DNA screening is an effective method to define the association between HPV infection and cervical cancer. Currently, exfoliated cervical cells are the ideal sample and have been widely used in cervical cancer screening, both for HPV testing and Pap testing [16]. While the majority of HPV infections are transient and eliminated by the immune system, persistent high risk HPV infection can progress into cervical intraepithelial neoplasia or invasive cancer. As such persistent high risk HPV infection is a critical step in the development of cervical neoplasia.
Recent studies have shown that HPV16 E6 variants are associated with persistence of viral infection and development of cervical lesions in western developed countries. In the current study, a large Chinese cohort was utilized to elucidate whether HPV16-specific variants are predictors for persistent HPV infection within the Chinese Han population. We sequenced samples from 292 patients and found six E6 gene variants, three E7 gene variants and nine E2 gene variants. Among the E6 variants, the variant T178G was detected in 139 transient HPV infections and 60 persistent HPV infections. Two other variants, T350G and A442C were detected in 4 transient HPV cases and 26 persistent HPV cases. Both variants were associated with persistent HPV16 infection. The rest of the E6 gene variants had no association with persistent HPV16 infection. To further investigate the relationship of HPV16 variants with persistent infection, the E2 and E7 genes were screened. There was no association between E7 variants and HPV16 infection. Among the nine variants in the E2 gene, both the C3158A and G3248A variants were associated with persistent HPV16 infection.
Although we identified several variants associated with persistent HPV16 infection, how these genetic mutations influence viral persistence is not clear at this time. One way in which these variants may influence persistence is that the missense mutations may allow for infected cells to evade the host’s immune system or alter their functional ability. It is likely that HPV variants in concert with HLA and other immune-genetic polymorphisms play a role in persistence and progression.
We have demonstrated that HPV16 variants are associated with the persistence of HPV16 infection in a population of women at risk for HPV infection. Additional prospective studies are being planned to use the identified variants to predict persistent HPV16 infection. Further studies on other HPV16 gene variants are necessary to determine whether the associations found in this study are explained by a direct effect that the E2 and E6 variations have on HPV16 infection, or if there is an interaction between these gene variants and other variations present within the genome. Future functional studies of mutated isolates would help evaluate the impact that these mutations have on HPV infection. Our findings demonstrate that genetic mutations in HPV are important in the progression of HPV infection. In clinical practice, the presence of these variants may argue for early treatment because of the likelihood of persistent HPV infection and possible progression to cervical neoplasia.
Acknowledgements
The study was supported by grants (PWRI2010_04) from the Public Health Bureau of Pudong new district, Shanghai and supported by grants from the National Natural Science Foundation of China (NSFC No. 81202044 and No. 81370074), the Science and Technology Commission of Shanghai Municipality (STCSM No. 12ZR1447600).
Disclosure of conflict of interest
None.
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