Human Papillomavirus Type 58 Genome Variations and RNA Expression in Cervical Lesions

Abstract

cHuman papillomavirus type 58 (HPV58) is relatively prevalent in China and other Asian countries. In this study, the HPV58 genome in cervical lesions was decoded from five grade 2 or 3 cervical intraepithelial neoplasia lesion (CIN2/3) samples and five cervical cancer tissues using rolling-circle amplification of total cell DNA and deep sequencing and verified by whole-genome cloning and sequencing. HPV58 isolates from China feature a total of 52 nucleotide substitutions (0.66%) from the reference HPV58 sequence, which appear mainly in two regions, with 12 from nucleotides (nt) 3430 to 4136 covering the E2/E4/E5 open reading frames (ORFs) and 13 from nt 4621 to 5540 covering the L2 ORF; these could be grouped as HPV58 Chinese Zhejiang-1, -2, and -3 (CNZJ-1, -2, and -3) according to their sequence similarities and restriction enzyme digestion. Phylogenetically, CNZJ-3 is similar to the reference HPV58 sublineage A1 sequence. The other two are close to sublineage A2. Analysis of cervical lesion-derived RNA revealed abundant HPV58 early transcripts spliced at the E6 and E1/E2 ORFs, where two 5= splice sites at nt 232 and nt 898 and two 3= splice sites at nt 510 and nt 3355 can be identified. Thus, our study represents the first genome-wide analysis of HPV58 and its expression in cervical lesions. Human papillomaviruses (HPVs) are causative agents in the development of cervical intraepithelial neoplasia (CIN) lesions and invasive carcinoma. Cervical persistent infection by high-risk HPV types is the single greatest risk factor for malignant progression (1, 2). Of 15 known high-risk HPV types, HPV16 and HPV18 are the two most common types inducing the development of cervical cancer (3-5). However, the prevalence of high-risk HPV58 infection displays considerable geographical variation (6). HPV58 was found in 3.3% of cervical cancers worldwide but in 5.6% of cervical cancers in Asia. HPV58 was detected in 7% of high-grade CIN lesions globally but in 12.2% in Asia (7,8). Studies from East Asian populations have shown that HPV58 infection ranks third in cervical cancer cases (7, 9). In China's Zhejiang area, HPV58 is more prevalent than HPV18 in CIN lesions (19.1% versus 5.4%), and equal infection frequencies of HPV58 and HPV18 are found in cervical cancers (9.4% each) (10). Similar to other high-risk HPVs (11-13), HPV58 integration in cervical lesions could occur by disruption of the viral E1 coding region (14).In this study, we performed comprehensive analyses of the HPV58 genome and transcriptome. The full complement of the viral genome was decoded using a rolling-circle amplification and deep sequencing (RCA-seq) technique, which does not require prior knowledge of the underlying genome. Viral RNA transcripts from total cell RNA were analyzed by means of directional ligation strand-specific RNA sequencing (DeLiseq) (15). Subsequently, three episomal HPV58 genomes were cloned and sequenced. A transcription map of the HPV58 early region was constructed from clinical CIN2 lesions. Our study represents the first genome-...

Oncogenic comparison of human papillomavirus type 58 E7 variants

“…In this regard, numerous studies have demonstrated that the epidemiologically high‐risk HPV16 E6 Asian‐American (AA) variant conferred a higher carcinogenic potential and, unlike other variants, its overexpression is sufficient to immortalize and transform primary human keratinocytes in the absence of E7 . In contrast to HPV16, studies on HPV58 biology are scarce . The only study on HPV58 variant available was performed to compare the transcriptional activity of the long control region of three HPV58 variants, and found that substitution of guanine to adenine residue at nucleotide position 7788 enhanced E6/E7 bistronic transcript promoter activity .…”

“…36 In contrast to HPV16, studies on HPV58 biology are scarce. 22,23 The only study on HPV58 variant available was performed to compare the transcriptional activity of the long control region of three HPV58 variants, and found that substitution of guanine to adenine residue at nucleotide position 7788 enhanced E6/E7 bistronic transcript promoter activity. 37 Our current study represents the very first investigation to describe and compare the oncogenic properties of the three most common naturally occurring HPV58 E7 variants.…”

“…The reason for such ethnogeographical specificity in the disease burden associated with HPV58 remains unknown. However, unlike HPV16 and 18 in which the oncogenicity is well‐established, studies on HPV58 biology are scarce . Current studies only show that HPV58 is less oncogenic than HPV16, but none of them focuses on investigating the oncogenicity of its variants.…”

The Impact of High-Risk HPV Genotypes Other Than HPV 16/18 on the Natural Course of Abnormal Cervical Cytology: A Korean HPV Cohort Study

“…HPV 58 accounts for a considerable disease burden in East Asia. Its prevalence in cervical cancer is higher in Asia (5.6%) than in other parts of the world (3.3%) [13]. In a large scale Korean study (n=1,650), HPV 58 was the second most common HPV in LSIL (8.1%) and HSIL (15.7%) [14].…”

“…The prevalence of HPV 58 increases significantly according to the severity of cervical neoplasia, and its variants are epidemiologically associated with a higher oncogenic risk [11]. Four featured variant lineages of HPV 58 (sublineage A1) showing a regional preponderance in Asia, and associated with a higher risk for cervical neoplasia, were recently reported [13,25]. Therefore, the detection of HPV 58 in addition to HPVs 16 and 18 in cytologically abnormal women may provide an early indicator of cervical precancerous lesion and invasive cancers in East Asia.…”