The study of the molecular biology of head and neck squamous cell carcinomas has been heavily reliant on the analysis of cell lines. This is largely because the maintenance of primary cell cultures is difficult. However, being monoclonal, cell lines are not representative of the primary tumor because of the loss of tumor cell heterogeneity. We report a technique for primary culture of squamous cell carcinomas with maintenance of epithelial and stromal cell components without overgrowth of the fibroblast cells. Phenotypic markers for fibroblasts and squamous cells were present up to 45 days after initiation of culture, and expression of epidermal growth factor receptor and involucrin in cultures paralleled that in the primary tumor. In vivo, tumor stromal elements are thought to play an important role in the support of epithelial cell growth. In the collagen gel system the preservation of the stromal cell component likely improves culture viability and growth. More importantly, this culture system allows the in vitro tumor to more accurately reflect the tumor from which it was derived, and it permits the study of primary squamous cell carcinomas under in vitro conditions.
The functional determinants for a good speech outcome after a partial tongue resection and reconstruction are not well established. The purpose of the present study was to assess the protrusion, grooving and symmetry of the tongue during sustained speech sound production using three‐dimensional ultrasound. The participants were twelve normal speakers and one partial glossectomee. The three‐dimensional ultrasound volumes of nine sustained speech sounds were measured in three sagittal planes. The data were re‐plotted as three‐dimensional surfaces. We calculated an anteriority index, a concavity index and an asymmetry index. The glossectomee's postoperative surface plots were characterized by asymmetry and convexity of the tongue surface. The anteriority index illustrated that the glossectomee's ability to protrude her tongue was not affected by the operation. The concavity index captured a decrease in midsagittal grooving in the glossectomee's tongue. The asymmetry index demonstrated height differences in the elevation of the right and left side of the tongue. We conclude that three‐dimensional ultrasound offers us a practical tool for the detailed and concise assessment of the lingual shape and deformation in patients undergoing glossectomy surgery.
Abstract Due to recent scientific advances, there is a growing demand for new indices with high fidelity to eliminate errors associated with certain index combinations and sequencing chemistries. These errors are due to insufficient edit distances (the minimum number of changes required to transform one index sequence to the other) between index sequences or index hopping. Recent publications have highlighted how sequencing reads are misassigned due to "index hopping" on Illumina patterned flow cells, such as the recently launched Illumina Novaseq which can generate billions of reads (>100 exomes) in a single run. This misassignment canlead to false positives in ultra-sensitive assays where low frequency variants or nucleic acid species are monitored. We have observed misassignment due to insufficient edit distance among Illumina TruSeq HT i7 indices at a frequency up to 1.5%. Therefore, we developed 968nt i7 indices that can be paired with the existing TruSeq HT i5 indices to achieve 768 high throughput dual combinations, which were validated using a novel method on both Illumina's 2- and 4-channel technologies as both single and dual indices. This method involved thepreparation of 96 libraries with unique, non-overlapping inserts to facilitate tracking of index misassignment. This allowed us to assess not only which index has misassigned library molecules, but also pinpoint the origin and rate of misassignment within a single run. With our 96 i7 indices, misassignment was observed at rates <0.1%. For even higher fidelity de-multiplexing, we have paired our 96 indices in a non-tandem manner for single use in both the i5 and i7 positions, known as Unique Dual Indices (UDIs). The use of UDIs further eliminates index read errors that misassign reads, enabling increased confidence in calling low frequency variants. UDIs can also eliminate PCR-induced chimerisms, which can significantly improve data from a variety of assays. We are validating 96 new indices as UDIs for avoidance of index hopping and for eliminating PCR-induced chimerism during multiplexed library amplification. Citation Format: Jonathan C. Irish, Jordan RoseFigura, Sukhinder K. Sandhu, Bita Carrion, Laurie Kurihara, Vladimir Makarov. Improved sample indexing for high fidelity demultiplexing to increase confidence in low frequency variant calling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1430.
Significance A significant proportion of head and neck cancer is driven by human papillomavirus (HPV) infection, and the expression of viral oncogenes is involved in the development of these tumors. However, the role of HPV integration in primary tumors beyond increasing the expression of viral oncoproteins is not understood. Here, we describe how HPV integration impacts the host genome by amplification of oncogenes and disruption of tumor suppressors as well as driving inter- and intrachromosomal rearrangements. Tumors that do and do not have HPV integrants display distinct gene expression profiles and DNA methylation patterns, which further support the view that the mechanisms by which tumors with integrated and nonintegrated HPV arise are distinct.
Summary CRISPR-Cas9 editing is a scalable technology for mapping of biological pathways, but it has been reported to cause a variety of undesired large-scale structural changes to the genome. We performed an arrayed CRISPR-Cas9 scan of the genome in primary human cells, targeting 17,065 genes for knockout with 101,029 guides. High-dimensional phenomics reveals a “proximity bias” in which CRISPR knockouts bear unexpected phenotypic similarity to knockouts of biologically-unrelated genes on the same chromosome arm, recapitulating both canonical genome structure and structural variants. Transcriptomics connects proximity bias to chromosome-arm truncations. Analysis of published large-scale knockout and knockdown experiments confirms that this effect is general across cell types, labs, Cas9 delivery mechanisms, and assay modalities, and suggests proximity bias is caused by DNA double-strand-breaks with cell cycle control in a mediating role. Finally, we demonstrate a simple correction for large-scale CRISPR screens to mitigate this pervasive bias while preserving biological relationships.
