Das Dipon, Hirayama Shun, Aye Ling, Bryan Michael E, Naegele Saskia, Zhao Brian, Efthymiou Vasileios, Mendel Julia, Fisch Adam S, Kröller Lea, Michels Birgitta E, Waterboer Tim, Richmon Jeremy D, Adalsteinsson Viktor, Lawrence Michael S, Crowson Matthew G, Iafrate A John, Faden Daniel L
Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts.
Massachusetts Eye and Ear, Boston, Massachusetts.
medRxiv. 2024 Feb 2:2024.01.04.24300841. doi: 10.1101/2024.01.04.24300841.
HPV-associated oropharyngeal cancer (HPV+OPSCC) is the most common HPV-associated cancer in the United States yet unlike cervical cancer lacks a screening test. HPV+OPSCCs are presumed to start developing 10-15 years prior to clinical diagnosis. Circulating tumor HPV DNA (ctHPVDNA) is a sensitive and specific biomarker for HPV+OPSCC. Taken together, blood-based screening for HPV+OPSCC may be feasible years prior to diagnosis.
We developed an HPV whole genome sequencing assay, HPV-DeepSeek, with 99% sensitivity and specificity at clinical diagnosis. 28 plasma samples from HPV+OPSCC patients collected 1.3-10.8 years prior to diagnosis along with 1:1 age and gender-matched controls were run on HPV-DeepSeek and an HPV serology assay.
22/28 (79%) of cases and 0/28 controls screened positive for HPV+OPSCC with 100% detection within four years of diagnosis and a maximum lead time of 7.8 years. We next applied a machine learning model classifying 27/28 cases (96%) with 100% detection within 10 years. Plasma-based PIK3CA gene mutations, viral genome integration events and HPV serology were used to orthogonally validate cancer detection with 68% (19/28) of the cohort having multiple cancer signals detected. Molecular fingerprinting of HPV genomes was performed across patients demonstrating that each viral genome was unique, ruling out contamination. In patients with tumor blocks from diagnosis (15/28), molecular fingerprinting was performed within patients confirming the same viral genome across time.
We demonstrate accurate blood-based detection of HPV-associated cancers with lead times up to 10 years before clinical cancer diagnosis and in doing so, highlight the enormous potential of ctDNA-based cancer screening.
人乳头瘤病毒相关的口咽癌（HPV+OPSCC）是美国最常见的人乳头瘤病毒相关癌症，但与宫颈癌不同的是，它缺乏筛查检测方法。HPV+OPSCC被认为在临床诊断前10 - 15年开始发展。循环肿瘤人乳头瘤病毒DNA（ctHPVDNA）是HPV+OPSCC的一种敏感且特异的生物标志物。综上所述，在诊断前数年进行基于血液的HPV+OPSCC筛查可能是可行的。
我们开发了一种人乳头瘤病毒全基因组测序检测方法HPV-DeepSeek，在临床诊断时具有99%的敏感性和特异性。对28份来自HPV+OPSCC患者的血浆样本进行检测，这些样本在诊断前1.3 - 10.8年采集，同时设置了年龄和性别1:1匹配的对照，对其进行HPV-DeepSeek检测和人乳头瘤病毒血清学检测。
28例病例中有22例（79%）以及28例对照中0例筛查出HPV+OPSCC呈阳性，在诊断后四年内检测率达100%，最长提前期为7.8年。接下来，我们应用机器学习模型对28例病例中的27例（96%）进行分类，在10年内检测率达100%。基于血浆的PIK3CA基因突变、病毒基因组整合事件和人乳头瘤病毒血清学被用于正交验证癌症检测，该队列中有68%（19/28）检测到多种癌症信号。对患者的人乳头瘤病毒基因组进行分子指纹分析，结果表明每个病毒基因组都是独特的，排除了污染。对于有诊断时肿瘤组织块的患者（15/28），在患者体内进行分子指纹分析，确认不同时间的病毒基因组相同。
我们证明了基于血液的人乳头瘤病毒相关癌症检测的准确性，在临床癌症诊断前最长可提前10年检测到，在此过程中，突出了基于ctDNA的癌症筛查的巨大潜力。
