Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway
- Cancer Research Malaysia, Malaysia
- Wellcome Trust Sanger Institute, United Kingdom
- Wellcome Trust Genome Campus, United Kingdom
- Moffitt Cancer Center, United States
- AstraZeneca, United Kingdom
Abstract
New therapeutic targets for oral squamous cell carcinoma (OSCC) are urgently needed. We conducted genome-wide CRISPR-Cas9 screens in 21 OSCC cell lines, primarily derived from Asians, to identify genetic vulnerabilities that can be explored as therapeutic targets. We identify known and novel fitness genes and demonstrate that many previously identified OSCC-related cancer genes are non-essential and could have limited therapeutic value, while other fitness genes warrant further investigation for their potential as therapeutic targets. We validate a distinctive dependency on YAP1 and WWTR1 of the Hippo pathway, where the lost-of-fitness effect of one paralog can be compensated only in a subset of lines. We also discover that OSCCs with WWTR1 dependency signature are significantly associated with biomarkers of favourable response towards immunotherapy. In summary, we have delineated the genetic vulnerabilities of OSCC, enabling the prioritization of therapeutic targets for further exploration, including the targeting of YAP1 and WWTR1.
Data availability
All main data generated or analysed during this study are included in the manuscript and supplementary files. Source data files for each figures and supplements have also been provided.The larger datasets of CRISPR screens, WES and RNA-sequencing output are available from Figshare (https://doi.org/10.6084/m9.figshare.11919753).
-
Genome-wide CRISPR screens reveal fitness genes in the Hippo pathway for oral squamous cell carcinomaFigshare, doi:10.6084/m9.figshare.11919753.
-
Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)cbioportal, doi:10.1038/nature14129.
Article and author information
Author details
Annie Wai Yeeng Chai
Funding
Medical Research Council (MR/P013457/1)
- Ultan McDermott
- Mathew J Garnett
- Sok Ching Cheong
Wellcome Trust (206194)
- Stacey Price
- Emanuel Gonçalves
- Fiona M Behan
- Jessica Bateson
- James Gilbert
- Mathew J Garnett
Cancer Research Malaysia (-)
- Annie Wai Yeeng Chai
- Pei San Yee
- Shi Mun Yee
- Hui Mei Lee
- Vivian KH Tiong
- Sok Ching Cheong
This work was directly supported by the Newton-Ungku Omar Fund and the Medical Research Council, United Kingdom (MR/P013457/1). Authors in S.C.C.'s group were supported by sponsors of Cancer Research Malaysia; Authors in M.J.G's group were supported by Wellcome. Other funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Chai et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 4,455
- views
-
- 547
- downloads
-
- 38
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway
eLife 9:e57761.
https://doi.org/10.7554/eLife.57761
Further reading
-
- Cancer Biology
- Medicine
A doctoral-level internship program was developed at the University of North Carolina at Chapel Hill with the intent to create customizable experiential learning opportunities for biomedical trainees to support career exploration, preparation, and transition into their postgraduate professional roles. We report the outcomes of this program over a 5-year period. During that 5-year period, 123 internships took place at over 70 partner sites, representing at least 20 academic, for-profit, and non-profit career paths in the life sciences. A major goal of the program was to enhance trainees’ skill development and expertise in careers of interest. The benefits of the internship program for interns, host/employer, and supervisor/principal investigator were assessed using a mixed-methods approach, including surveys with closed- and open-ended responses as well as focus group interviews. Balancing stakeholder interests is key to creating a sustainable program with widespread support; hence, the level of support from internship hosts and faculty members were the key metrics analyzed throughout. We hypothesized that once a successful internship program was implemented, faculty culture might shift to be more accepting of internships; indeed, the data quantifying faculty attitudes support this. Furthermore, host motivation and performance expectations of interns were compared with results achieved, and this data revealed both expected and surprising benefits to hosts. Data suggests a myriad of benefits for each stakeholder group, and themes are cataloged and discussed. Program outcomes, evaluation data, policies, resources, and best practices developed through the implementation of this program are shared to provide resources that facilitate the creation of similar internship programs at other institutions. Program development was initially spurred by National Institutes of Health pilot funding, thereafter, successfully transitioning from a grant-supported model, to an institutionally supported funding model to achieve long-term programmatic sustainability.
-
- Cancer Biology
For traditional laboratory microscopy observation, the multi-dimensional, real-time, in situ observation of three-dimensional (3D) tumor spheroids has always been the pain point in cell spheroid observation. In this study, we designed a side-view observation petri dish/device that reflects light, enabling in situ observation of the 3D morphology of cell spheroids using conventional inverted laboratory microscopes. We used a 3D-printed handle and frame to support a first-surface mirror, positioning the device within a cell culture petri dish to image cell spheroid samples. The imaging conditions, such as the distance between the mirror and the 3D spheroids, the light source, and the impact of the culture medium, were systematically studied to validate the in situ side-view observation. The results proved that placing the surface mirror adjacent to the spheroids enables non-destructive in situ real-time tracking of tumor spheroid formation, migration, and fusion dynamics. The correlation between spheroid thickness and dark core appearance under light microscopy and the therapeutic effects of chemotherapy doxorubicin and natural killer cells on spheroids’ 3D structure was investigated.
