Identification of Specific Tumor Markers in Vulvar Carcinoma Through Extensive Human Papillomavirus DNA Characterization Using Next Generation Sequencing Method

Abstract

Objectives A subset of vulvar carcinomas (VC) are associated with human papillomavirus (HPV) DNA. This trait can be used to identify tumor markers for patient's follow-up. A large diversity of HPV prevalence in VC has been reported, but no data are available concerning the insertional HPV status in this tumor type. Therefore, we have used an innovative next generation sequencing (NGS)-based CaptHPV method able to provide an extensive characterization of HPV DNA in tumors. Material and Methods Tumor tissue specimens from 55 patients with VC were analyzed using p16 immunohistochemistry, in situ hybridization, polymerase chain reaction, and CaptHPV-NGS assays. Results Our analyses showed that 8 (14.5%) of 55 cases were associated with HPV 16 DNA. No other HPV genotypes were identified. The HPV genome was in a free episomal state only in one case and both episomal and integrated into the tumor cell genome in 7. There was a single insertion in 5 cases and multiple sites, scattered at different chromosomal loci in two. ISH data suggest that some of these might reflect tumor heterogeneity. Viral integration targeted cellular genes among which were TP63, CCDC148, LOC100133091, PKP1, and POLA2. Viral integration at the PKP1 locus was associated with partial gene deletion, and no PKP1 protein was detected in tumor tissue. Conclusions Using the NGS-based innovative capture-HPV approach, we established a cartography of HPV 16 DNA in 8 VC cases and identified novel genes targeted by integration that may be used as specific tumor markers. In addition, we established a rationale strategy for optimal characterization of HPV status in VC.

Human papilloma virus (HPV) integration signature in Cervical Cancer: identification of MACROD2 gene as HPV hot spot integration site

“… 33 HPV integration in TP63 genes was recently reported in HPV-positive vulvar cancer patients. 34 In another HPV-positive head and neck squamous cell carcinoma study, HPV sites of integration into MIPOL1/TTC6 were identified in more than one tumour sample. The integration of HPV into the ERBB2 gene site was observed in two patients in association with ERBB2 amplifications, in concordance with previous reports.…”

Genome-wide association study of aromatase inhibitor discontinuation due to musculoskeletal symptoms

“…In the primary GWAS analysis, the T allele of the intronic rs79048288 variant within CCDC148 was associated with a 4.4-fold higher AIMSS risk and the G allele of the intergenic rs912571 upstream of PPP1R14C was associated with a 3.3-fold lower AIMSS risk. In silico analyses did not reveal any obvious functional impact of the intronic variant within CCDC148 (rs79048288), and little is known about the physiological function of this protein, except that dysregulated expression has been reported in several cancer types 38,39 . In silico analyses revealed that the G allele of rs912571 was associated with higher expression of PPP1R14C in sun-exposed skin, indicating that this variant could be functionally consequential.…”

A non-small cell lung carcinoma patient responded to crizotinib therapy after alectinib-induced interstitial lung disease

“…本例除 EML4 - ALK 外同时存在其他 ALK 融合基因（ CCDC148 - ALK 、 PKDCC - ALK 和 VIT - ALK ）。截至目前，已经发现了许多非 EML4 的 ALK 融合伴侣 ［ 4 ］ 。有文献报道， VIT - ALK 是对阿来替尼敏感的融合基因， PKDCC - ALK 融合是对 ALK -TKI WX-0593敏感的融合基因 ［ 30 - 31 ］ 。本例报道NSCLC患者中存在 CCDC148 - ALK 融合，一般 CCDC148 与妇科肿瘤相关 ［ 32 ］ 。本文资料中，NSCLC患者在阿来替尼治疗期间 CCDC148 - ALK 显著清除，推测 CCDC148 - ALK 可能是对阿来替尼敏感的融合基因，但仍须进一步研究证明。…”