Comparison of variant-specific hybridization and single-strand conformational polymorphism methods for detection of mixed human papillomavirus type 16 variant infections

Variation of HPV Subtypes with Focus on HPV-Infection and Cancer in the Head and Neck Region

The human papillomavirus (HPV) comprises a heterogeneous group of double-strand DNA viruses with variable potential to infect human epithelial cells and trigger neoplastic transformation. Its 8 kb genome encodes proteins required for virus replication and self-organized formation of infectious particles but also for early proteins E6 and E7 able to trigger neoplastic transformation. E6 and E7 of high-risk (HR) HPV subtypes can bind to p53 or release E2F and abrogate replication control. Due to variable amino acid sequence (AAS) in the binding sites of E6 and E7 particular HR-HPV variants within subtypes are essentially heterogeneous in efficacy triggering neoplastic transformation and cancer development. This could explain differences in the clinical course of HPV-driven head and neck cancer.

Differences and changes in human papillomavirus type 16 variant status in human immunodeficiency virus-positive adults are not uncommon

Human papillomavirus type 16 (HPV-16) genotype variants have been the subject of several investigations, but study participants have rarely been sampled more than once. In this study, among a cohort of human immunodeficiency virus (HIV)-infected adults, HPV-16 variants were investigated in samples collected concurrently from the anus and cervix, as well as in serial samples collected from the same anatomical site at 12-month intervals. HPV-16 variants in stored extracts of cervical and anal samples were determined from subjects with multiple visits and at least one sample positive for HPV-16. Seven polymorphic nucleotide positions within the E6 region were analysed by pyrosequencing to determine genotype variants. Of 364 samples examined, 176 anal and 39 cervical swabs from 84 different subjects yielded unequivocal sequences of eight major HPV-16 variants. Eight samples contained probable novel HPV-16 variants and in one sample two variants were detected. In eight out of 29 (27.6%) anal-cervical sample pairs positive for HPV-16, discordant variants were found. From 57 anal and nine cervical sample series of HPV-16-positive samples, a change in HPV-16 variant status over time was seen in nine (13.6%) instances (seven anal and two cervical) from eight different participants. Changes in HPV-16 variants in HIV-infected adults were seen most frequently when different anatomical sites were sampled, but were also observed over time.

Genomic diversity of human papillomavirus (HPV) genotype 38

Human papillomavirus (HPV) genotype HPV 38 is a HPV genotype associated with skin cancer and is classified taxonomically in the beta-PV genus-species 2. At least six genomic variants of HPV 38, including prototype isolate and its subtype FA125, have been characterized so far. In order to investigate further the genomic diversity of HPV 38, a total of 39 HPV 38 positive samples obtained from hairs plucked from pubic, scrotal, perianal or eyebrow regions from 31 immunocompetent healthy male individuals were analyzed. The characterization of genomic variants was based on analysis of L1, E6, and E7 genomic regions. Sequence analysis revealed the presence of a single genomic variant in 35 samples and the presence of at least two different HPV 38 genomic sequences in four samples. A total of nine, nine, and five L1, E6, and E7 genomic variants were identified among 35 isolates, respectively. After combining nucleotide variations in all three genomic regions for a particular isolate, 13 different variants were identified, of which 6 and 7 corresponded to HPV 38 and FA125, respectively. In addition to 5 genomic variants identified previously (prototype isolate, subtype FA125, putative subtype AF091444, isolates U21875 and AF091443), 12 novel genomic variants were characterized. A sixth genomic variant described previously (L38917) was found to be identical with prototype HPV 38 isolate. Taking into account the results of this and previous studies, at least seventeen HPV 38 genomic variants exist today, 12 of which are described for the first time in this study.

Human papillomavirus type 18 variant lineages in United States populations characterized by sequence analysis of LCR-E6, E2, and L1 regions

While HPV 16 variant lineages have been well characterized, the knowledge about HPV 18 variants is limited. In this study, HPV 18 nucleotide variations in the E2 hinge region were characterized by sequence analysis in 47 control and 51 tumor specimens. Fifty of these specimens were randomly selected for sequencing of an LCR-E6 segment and 20 samples representative of LCR-E6 and E2 sequence variants were examined across the L1 region. A total of 2770 nucleotides per HPV 18 variant genome were considered in this study. HPV 18 variant nucleotides were linked among all gene segments analyzed and grouped into three main branches: Asian-American (AA), European (E), and African (Af). These three branches were equally distributed among controls and cases and when stratified by Hispanic and non-Hispanic ethnicities. Among invasive cervical cancer cases, no significant differences in the three HPV variant branches were observed among ethnic groups or when stratified by histopathology (squamous vs. adenocarcinoma). The Af branch showed the greatest nucleotide variability when compared to the HPV 18 reference sequence and was more closely related to HPV 45 than either AA or E branches. Our data also characterize nucleotide and amino acid variations in the L1 capsid gene among HPV 18 variants, which may be relevant to vaccine strategies and subsequent studies of naturally occurring HPV 18 variants. Several novel HPV 18 nucleotide variations were identified in this study.

Mutation of RET gene in Chinese patients with Hirschsprung’s disease

AIM: To investigate the pathogenic mechanism of Hirschsprung’s disease (HD) at the molecular level and to elucidate the relationship between RET oncogene and Chinese patients with HD.

METHODS: Exon 13 of RET oncogene from 20 unrelated HD patients was analyzed with polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). The positive amplifying products were then sequenced. According to the results of SSCP and DNA sequence, SSCP was done as well for the samples from the family other members of some cases with mutated RET gene.

RESULTS: SSCP analysis indicated that mobility abnormality existed in 4 unrelated HD patients. Direct DNA sequence analysis identified a missense mutation, T to G at the nucleotide 18888 and a frameshift mutation at the nucleotide 18926 insG. In a HD family, the sicked child and his father were the same heterozygous missense mutation (T to G at nucleotide 18888).

CONCLUSION: Among Chinese HD patients, RET gene mutations may exist in considerable proportion with different patterns. These new discoveries indicate that RET mutations may play an important role in the pathogenesis of unrelated HD in the Chinese population. PCR-SSCP combined with DNA sequence can be used as a tool in the genetic diagnosis of HD.

Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix

Human papillomaviruses (HPV) are strongly associated with cervical intraepithelial neoplasia (CIN) and invasive cancer mainly through the action of the E6 and E7 viral proteins, transcription of which is down-regulated by the E2 protein. To test the hypothesis that HPV 16 E2 variation is important in the development of high-grade squamous neoplasia of the cervix, we carried out a cross-sectional analysis of low-grade and high-grade squamous intraepithelial lesions (SILs) for specific mutations in the HPV 16 E2 gene and for E2 gene disruption in these regions. Isolates were also analysed for the HPV 16 350T-G variant. 22 of 178 low-grade SILs and 43 of 61 high-grade SILs examined, contained HPV 16. No relationship was found between the E6 350T-G variant, or the E2 hinge region 3410C-T variant, and lesion grade. However, disruption of the regions of E2 analysed was significantly more frequent in high-grade lesions, and there was a significant association between the 3684C-A variant in the E2 DNA binding domain and high-grade histology suggesting that this variant may be important in progression to high-grade intraepithelial disease.

Diagnosing human papillomaviruses: recent advances

The biological importance of a group of human papillomaviruses, known as high-risk human papillomaviruses, as the key causal agent for almost all cervical cancer has now been established. Many aspects of the natural history of high-risk human papillomaviruses as sexually transmitted infections and as oncogenic agents have been researched. Although human papillomavirus diagnosis is largely confined to DNA detection techniques in cervical smears, there is accumulating evidence that the best polymerase chain reaction and hybrid capture techniques are more sensitive and probably of similar specificity compared with cervical cytology as a triage test for women with borderline smear abnormalities and for screening older women. This is strong presumptive evidence that high-risk human papillomavirus testing could be useful in cervical screening. Current research is aimed at establishing a place for high-risk human papillomavirus testing in routine screening practice. Randomised clinical trials, long-term natural history studies, mathematical modelling, and economic and psychosocial studies are being used to demonstrate whether this testing can improve both the effectiveness and efficiency of cervical screening in a range of situations.