Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington.
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
Clin Cancer Res. 2018 Jun 15;24(12):2828-2843. doi: 10.1158/1078-0432.CCR-17-1339. Epub 2018 Mar 29.
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with high mortality and a lack of targeted therapies. To identify and prioritize druggable targets, we performed genome analysis together with genome-scale siRNA and oncology drug profiling using low-passage tumor cells derived from a patient with treatment-resistant HPV-negative HNSCC. A tumor cell culture was established and subjected to whole-exome sequencing, RNA sequencing, comparative genome hybridization, and high-throughput phenotyping with a siRNA library covering the druggable genome and an oncology drug library. Secondary screens of candidate target genes were performed on the primary tumor cells and two nontumorigenic keratinocyte cell cultures for validation and to assess cancer specificity. siRNA screens of the kinome on two isogenic pairs of p53-mutated HNSCC cell lines were used to determine generalizability. Clinical utility was addressed by performing drug screens on two additional HNSCC cell cultures derived from patients enrolled in a clinical trial. Many of the identified copy number aberrations and somatic mutations in the primary tumor were typical of HPV(-) HNSCC, but none pointed to obvious therapeutic choices. In contrast, siRNA profiling identified 391 candidate target genes, 35 of which were preferentially lethal to cancer cells, most of which were not genomically altered. Chemotherapies and targeted agents with strong tumor-specific activities corroborated the siRNA profiling results and included drugs that targeted the mitotic spindle, the proteasome, and G-M kinases and We also show the feasibility of drug profiling for patients enrolled in a clinical trial. High-throughput phenotyping with siRNA and drug libraries using patient-derived tumor cells prioritizes mutated driver genes and identifies novel drug targets not revealed by genomic profiling. Functional profiling is a promising adjunct to DNA sequencing for precision oncology. .
头颈部鳞状细胞癌（HNSCC）是全球第六大常见癌症，死亡率高，缺乏靶向治疗方法。为了鉴定和优先考虑可用药的靶点，我们使用源自一位治疗耐药 HPV 阴性 HNSCC 患者的低传代肿瘤细胞，进行了基因组分析以及全基因组规模的 siRNA 和肿瘤药物分析。建立了肿瘤细胞培养物，并进行了全外显子组测序、RNA 测序、比较基因组杂交以及针对可用药基因组和肿瘤药物库的高通量表型分析。在原代肿瘤细胞和两个非致瘤角质形成细胞培养物上对候选靶基因进行了二次筛选，以验证和评估癌症特异性。对两个 p53 突变的 HNSCC 细胞系的同源对进行了激酶组 siRNA 筛选，以确定通用性。通过对来自参加临床试验的两名 HNSCC 患者的另外两个细胞培养物进行药物筛选，解决了临床实用性问题。原代肿瘤中许多鉴定的拷贝数异常和体细胞突变是 HPV(-) HNSCC 的典型特征，但没有指向明显的治疗选择。相比之下，siRNA 谱分析鉴定出 391 个候选靶基因，其中 35 个对癌细胞具有优先致死性，其中大多数基因没有发生改变。具有强烈肿瘤特异性活性的化疗药物和靶向药物证实了 siRNA 谱分析结果，其中包括靶向有丝分裂纺锤体、蛋白酶体和 G-M 激酶的药物。我们还展示了针对参加临床试验的患者进行药物谱分析的可行性。使用源自患者的肿瘤细胞进行的 siRNA 和药物文库高通量表型分析优先考虑了突变的驱动基因，并确定了基因组分析未揭示的新药物靶点。功能分析是精准肿瘤学中 DNA 测序的有前途的辅助手段。
