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Supplementary Table 8

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Supplementary Table 10

Supplementary Table 4

Supplementary Table 5

Supplementary Table 1, 2, 3

Supplementary Figures

Purpose: 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.Experimental Design: 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.Results: 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 G2–M kinases WEE1 and CHK1. We also show the feasibility of ex vivo drug profiling for patients enrolled in a clinical trial.Conclusions: 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. Clin Cancer Res; 24(12); 2828–43. ©2018 AACR.

Supplementary Table 9

The progressive, late-onset, nonsyndromic, sensorineural hearing loss (PNSHL) is the most common cause of sensory impairment globally, with presbycusis affecting greater than a third of individuals over the age of 65. The etiology underlying PNSHL include presbycusis, noise-induced hearing loss, drug ototoxicity, and delayed-onset autosomal dominant hearing loss (AD PNSHL). The objective of this article is to discuss the potential diagnostic and therapeutic applications of genomic medicine in PNSHL. Genomic factors contribute greatly to PNSHL. The heritability of presbycusis ranges from 25 to 75%. Current therapies for PNSHL range from sound amplification to cochlear implantation (CI). PNSHL is an excellent candidate for genomic medicine approaches as it is common, has well-described pathophysiology, has a wide time window for treatment, and is amenable to local gene therapy by currently utilized procedural approaches. AD PNSHL is especially suited to genomic medicine approaches that can disrupt the expression of an aberrant protein product. Gene therapy is emerging as a potential therapeutic strategy for the treatment of PNSHL. Viral gene delivery approaches have demonstrated promising results in human clinical trials for two inherited causes of blindness and are being used for PNSHL in animal models and a human trial. Non-viral gene therapy approaches are useful in situations where a transient biologic effect is needed or for delivery of genome editing reagents (such as CRISPR/Cas9) into the inner ear. Many gene therapy modalities that have proven efficacious in animal trials have potential to delay or prevent PNSHL in humans. The development of new treatment modalities for PNSHL will lead to improved quality of life of many affected individuals and their families.

This study maps the cellular response to the WEE1 inhibitor and explores the contributions of p53 to its effect.

Maximum two-dimensional (2D) diameter has been used to define giant pituitary adenoma (GPA) surgery outcomes as has volume using an ellipsoid approximation of volumetrics. Cross sectional length can be measured in several different planes. We sought to compare the accuracy of different 2D cross sectional measurements with the 3D volumetric measurements for predicting GPA surgery outcomes.Retrospective analysis was performed on a prospectively collected database. Tumors with3 cm diameter were identified and classified based on maximal cross sectional measurements in three separate co-axial planes, i.e. transverse (TV), antero-posterior (AP) and cranio-caudal (CC). Volume was calculated using both MRI-guided volumetrics and an ellipsoid approximation (TV × AP × CC/2). Univariate and multivariate analysis was used to evaluate the relationship between cross sectional and volumetric data and extent of resection (EOR).In 62 subjects, median tumor volume using 3D volumetrics was 13.74 cm(3), which was overestimated by 16 % by the ellipsoid calculation (p = 0.0029), particularly for tumors20 cm(3). Gross total resection (GTR) was 46.7 % and median EOR was 99.57 %. At 22-month follow-up, visual and anterior pituitary functions were stable (90 %) or improved (87 %). Pre-operative tumor volume10 cm(3) (p = 0.02) and Knosp grade 3-4 (p = 0.04) were independent predictors of EOR. Knosp grade 3-4 (p 0.0001), TV measurement4 cm (p = 0.007) and maximum cross sectional length4 cm (p = 0.04) were predictors of not achieving GTR. Only TV measurement (p = 0.02) predicted permanent diabetes insipidis. The smallest significant thresholds for predicting decreased GTR were TV measurement25 mm, AP measurement35 mm and volume19 cm(3).We propose a new volumetric threshold of 20 cm(3) as most accurate for predicting GTR in the EEA era. CC measurement is the least useful predictor. Cavernous sinus invasion remains the best predictor of incomplete resection.