Abstract 1111: Altered inflammatory and death pathways in head and neck cell lines model genomic and expression signatures identified in The Cancer Genome Atlas
Authors: Yang Xinping , Cheng Hui , Saleh Anthony , Cornelius Shaleeka , Guven-Maiorov Emine , Nussinov Ruth , Van Weas Carter , Chen Zhong , Keskin Ozlem , Gursoy Attila 
Published: August 2015

The Cancer Genome Atlas (TCGA) project has investigated 279 HNSCC tissue specimens, and uncovered significant genomic alterations of key molecules involved in inflammation, NF-KB, and death pathways. These genetic alterations include amplification of FADD (11q13) and BIRC2/3 (11q22), mutations of caspase 8 and RIPKs in HPV(-), or deletion of TRAF3 in HPV(+) HNSCC tissues. Using bioinformatic analyses and protein structural and interactive tools, we identified ∼60 proteins that may potentially interact with these genetically altered molecules involved in the inflammation and death pathways. More than 90% HNSCC tissues studied in TCGA exhibited expression or genetic alterations of these genes, with FADD amplification and/or overexpression ranking first with 37%. We also searched this group of genes among more than 20 major cancer types investigated by TCGA, among which HNSCC ranked the highest for the alterations. To further investigate and identify experimental models for functional studies of these genetic and phenotypic alterations, we have performed whole transcriptome (RNA-seq) and genome-wide exome DNA sequencing (exome DNA-seq) in 15 HPV(-) and 11 HPV(+) HNSCC lines, and compared them with three normal human oral mucosa lines and 8 matched blood samples. We have identified gene amplifications and overexpression among many of the molecules involved in inflammation, NF-KB and death pathways in cell lines, which were observed in the HNSCC TCGA project. Among the top 22 genes identified from TCGA with the alteration rate greater than 8% in cancer tissues, we found consistent expression patterns of ∼77% molecules in our cell lines. To further test the function of these molecules, we established HNSCC cell lines stably transfected with a vector that contains NF-κB transcription factor response elements upstream of the β-lactamase reporter gene, to measure a fluorescence resonance energy transfer (FRET) substrate cleaved by β-lactamase, that results in blue fluorescence. Using these NF-KB reporter cell lines, large RNAi screening assays have been performed to assess the regulatory and signaling molecules involve in NF-κB and death pathways to model the findings from TCGA. The function and mechanistic validation of these molecules are under the way, which could provide precise molecular targets of diagnosis and prognosis for further preclinical and clinical investigation in HNSCC.

Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74; and funded under contract HHSN261200800001E

Citation Format: Xinping Yang, Hui Cheng, Anthony Saleh, Shaleeka Cornelius, Emine Guven-Maiorov, Ruth Nussinov, Carter Van Weas, Zhong Chen, Ozlem Keskin, Attila Gursoy. Altered inflammatory and death pathways in head and neck cell lines model genomic and expression signatures identified in The Cancer Genome Atlas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1111. doi:10.1158/1538-7445.AM2015-1111