HNSCC PDX Engraftment: Aligned Sequencing Reads

This dataset includes 112 head and neck tumour samples with matched normal (blood) samples sequenced using a custom hybrid capture panel.

Description: Overall survival remains very poor for patients diagnosed as having head and neck squamous cell carcinoma (HNSCC). Identification of additional biomarkers and novel therapeutic strategies are important for improving patient outcomes. Patient-derived xenografts (PDXs), generated by implanting fresh tumor tissue directly from patients into immunodeficient mice, recapitulate many of the features of their corresponding clinical cancers, including histopathological and molecular profiles. Using a large collection of PDX models of HNSCC, we demonstrate that rapid engraftment into immunocompromised mice is highly prognostic and show that genomic deregulation of the G1/S checkpoint pathway correlates with engraftment. Furthermore, CCND1 and CDKN2A genomic alterations are predictive of response to the CDK4and CDK6 inhibitor abemaciclib. Overall, our study supports the pursuit of CDK4 and CDK6 inhibitors as a therapeutic strategy for a substantial proportion of HNSCC patients and demonstrates the potential of using PDX models to identify targeted therapies that will benefit patients who have the poorest outcomes.
Authors: Christina Karamboulas, Jeffrey P. Bruce, Andrew J. Hope, Jalna Meens, Shao Hui Huang, Natalie Erdmann, Elzbieta Hyatt, Keira Pereira, David P. Goldstein, Ilan Weinreb, Jie Su, Brian O’Sullivan, Rodger Tiedemann, Fei-Fei Liu, Trevor J. Pugh, Scott V. Bratman, Wei Xu, Laurie Ailles
Lab: Pugh
Year: 2018
Keywords: head and neck squamous cell carcinoma, HNSCC, personalized treatment, targeted sequencing, cancer, PDX

Citation

Christina Karamboulas, Jeffrey P. Bruce, Andrew J. Hope, Jalna Meens, Shao Hui Huang, Natalie Erdmann, Elzbieta Hyatt, Keira Pereira, David P. Goldstein, Ilan Weinreb, Jie Su, Brian O’Sullivan, Rodger Tiedemann, Fei-Fei Liu, Trevor J. Pugh, Scott V. Bratman, Wei Xu, Laurie Ailles. Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma. Cell Reports. Volume 25, Issue 5. (2018) Pages 1318-1331.e4, https://doi.org/10.1016/j.celrep.2018.10.004

224 samples

Sample Type:primary tumour tissue
Species:Human
Datatype:scRNAseq
Technology:scRNA-seq

Contact

This dataset is public.

Contact: Jeff Bruce

Contact email: Email