晚期阴茎鳞状细胞癌（pSCC）是一种罕见且侵袭性的恶性肿瘤，免疫检查点抑制剂（ICIs）的疗效有限。大约一半的pSCC与人类乳头状瘤病毒（HPV）感染相关。我们回顾性评估了Caris Life Sciences数据集中pSCC体内变异和ICIs相关生物标志物的情况，旨在建立与HPV依赖的肿瘤发生相关的特征。使用DNA和RNA的下一代测序（NGS）对pSCC肿瘤进行分析。免疫组化（IHC）评估了程序性死亡配体1（PD-L1）的表达。通过片段分析、IHC（SP142；≥1%）和NGS对微卫星不稳定性（MSI）进行了测试。肿瘤突变负荷（TMB）高定义为≥10个突变/Mb。当可用时，使用全外显子测序（WES）确定HPV16/18状态。多个比较进行了显著性调整（q值<.05）。NGS的整体队列（N = 108）显示TP53（46%）、CDKN2A（26%）和PIK3CA（25%）是最常见的突变。总体而言，51%的肿瘤为PD-L1阳性，10.7%具有高TMB，1.1%具有错配修复缺陷（dMMR）/MSI高状态。29位患者通过WES获得HPV状态（HPV16/18+，n = 13；HPV16/18-，n = 16）。KMT2C突变（33% vs. 0%）和FGF3扩增（30.8% vs. 0%）仅在HPV16/18+肿瘤中存在，而CDKN2A突变（0% vs. 37.5%）仅在HPV16/18-肿瘤中存在。只有HPV16/18+组中有TMB高（30.8%）。两组具有可比性的PD-L1和dMMR/MSI-H状态。通过对pSCC中体内变异的大规模和全面的NGS评估，我们发现HPV16/18+与HPV16/18- pSCCs是分子上不同的肿瘤。我们发现TMB高仅在HPV16/18+肿瘤中存在，需要在较大的数据集中进行确认。阴茎鳞状细胞癌（pSCC）是晚期状态下的一种罕见且侵袭性的恶性肿瘤，预后差，全选患者应用ICIs疗效有限。人类乳头状瘤病毒（HPV）感染是pSCC的已知危险因素，其对基因组肿瘤分析的影响尚未明确。通过下一代测序，我们探索了pSCC和HPV驱动的致癌分子标志物的遗传景观。我们的结果显示，HPV阳性和HPV阴性的pSCC是分子上不同的肿瘤。肿瘤突变负荷的增加与HPV阳性肿瘤相关，并且可作为预测ICI疗法治疗反应的生物标志物。我们的结果支持日益增多的文献，表明在ICI疗法临床试验中可使用pSCC的HPV状态来指导患者分层。©2023美国癌症学会。

Advanced penile squamous cell carcinoma (pSCC) is a rare and aggressive malignancy with limited success of immune-checkpoint inhibitors (ICIs). Approximately half of pSCC cases are associated with human papillomavirus (HPV) infection.Evaluation was done retrospectively of the landscape of somatic alterations and ICI-related biomarkers in pSCC by using the Caris Life Sciences data set with the aim to establish signatures for HPV-dependent oncogenesis. The pSCC tumors were analyzed by using next-generation sequencing (NGS) of DNA and RNA. Programmed death ligand 1 (PD-L1) expression was evaluated by immunohistochemistry (IHC). Microsatellite instability (MSI) was tested by fragment analysis, IHC (SP142; ≥1%), and NGS. Tumor mutational burden (TMB)-high was defined as ≥10 mutations/Mb. HPV16/18 status was determined by using whole-exome sequencing (WES) when available. Significance was adjusted for multiple comparisons (q value < .05).NGS of the overall cohort (N = 108) revealed TP53 (46%), CDKN2A (26%), and PIK3CA (25%) to be the most common mutations. Overall, 51% of tumors were PD-L1+, 10.7% had high TMB, and 1.1% had mismatch repair-deficient (dMMR)/MSI-high status. Twenty-nine patients had their HPV status made available by WES (HPV16/18+, n = 13; HPV16/18-, n = 16). KMT2C mutations (33% vs. 0%) and FGF3 amplifications (30.8% vs. 0%) were specific to HPV16/18+ tumors, whereas CDKN2A mutations (0% vs. 37.5%) were exclusive to HPV16/18- tumors. TMB-high was exclusively found in the HPV16/18+ group (30.8%). The two groups had comparable PD-L1 and dMMR/MSI-H status.In a large and comprehensive NGS-based evaluation of somatic alterations in pSCC, HPV16/18+ versus HPV16/18- pSCCs were molecularly distinct tumors. Our finding that TMB-high is exclusive to HPV16/18+ tumors requires confirmation in larger data sets.Penile squamous cell carcinoma (pSCC) is a rare and aggressive malignancy in the advanced setting, with poor prognosis and little success with immune-checkpoint inhibitors (ICIs) in an unselected patient approach. Human papillomavirus (HPV) infection is a known risk factor for pSCC; its impact on genomic tumor profiling is less defined. Using next-generation sequencing, we explored the genetic landscape and ICI-related biomarkers of pSCC and HPV-driven oncogenic molecular signatures. Our results indicate that HPV-positive and HPV-negative pSCCs are molecularly distinct tumors. Increased tumor mutational burden is associated with HPV-positive tumors, and could serve as a biomarker for predicting therapeutic response to ICI-based therapies. Our results support the growing literature indicating that HPV status in pSCC can be used to guide patient stratification in ICI-based clinical trials.© 2023 American Cancer Society.