Background: To extend the practicality of liquid biopsy beyond the historical HPV circulating tumor DNA (ctDNA) assays, we evaluated the clinical relevance of a novel next-generation sequencing HPV ctDNA assay in patients with locally advanced and metastatic squamous cell cancer of the anal canal (mSCCA). Methods: ctDNA isolated from the plasma of patients with mSCCA was sequenced using a 1.4 Mb hybrid-capture target-enrichment panel covering the whole genome sequences of all 193 HPV types. The HPV type, copy number (CN), and integration sites were determined using a bioinformatic pipeline. Results: A total of 77 plasma samples from 28 patients with HPV-related SCCA were retrospectively analyzed. HPV ctDNA was detected in 26 cases (93%) (including uncommon subtypes). The median HPV CN was higher in metastatic versus locally recurrent/unresectable SCCA (p= 0.043). Changes in the HPV CN were concordant with the radiographic response (p= 0.027). An integration event was detected in 23 patients (82%), with presumed episomal HPV DNA present in the remaining patients. Higher HPV integration (a mean of ≥1 integration across samples) was associated with a worse overall survival from the start of immunotherapy (13.6 months versus 36.0 months;p= 0.003). Conclusions: Using HPV-informed next-generation sequencing of the ctDNA, we found changes in the HPV CN correlated with the treatment response and that HPV integration detected in the ctDNA is an unfavorable prognostic biomarker.
背景：为拓展液体活检在传统人乳头瘤病毒（HPV）循环肿瘤DNA（ctDNA）检测之外的临床应用，本研究评估了一种新型二代测序HPV ctDNA检测在局部晚期及转移性肛管鳞状细胞癌（mSCCA）患者中的临床意义。方法：从mSCCA患者血浆中分离ctDNA，采用覆盖193种HPV全基因组序列的1.4 Mb杂交捕获靶向富集测序面板进行测序，通过生物信息学流程确定HPV分型、拷贝数（CN）及整合位点。结果：对28例HPV相关SCCA患者的77份血浆样本进行回顾性分析，其中26例（93%）检出HPV ctDNA（包含罕见亚型）。转移性SCCA患者的HPV中位CN显著高于局部复发/不可切除SCCA患者（p=0.043）。HPV CN变化与影像学疗效评估结果具有一致性（p=0.027）。23例患者（82%）检测到HPV整合事件，其余患者存在推测的游离型HPV DNA。较高HPV整合水平（样本平均整合数≥1）与免疫治疗开始后较差的总生存期显著相关（13.6个月 vs 36.0个月；p=0.003）。结论：通过ctDNA的HPV靶向二代测序，我们发现HPV CN变化与治疗反应相关，且ctDNA中检测到的HPV整合是不良预后的生物标志物。
肿瘤(癌症)患者之家