Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

We have recently performed the characterization of alternative splicing events (ASEs) in head and neck squamous cell carcinoma, which allows dysregulation of protein expression common for cancer cells. Such analysis demonstrated a high ASE prevalence among tumor samples, including tumor-specific alternative splicing in the GSN gene.In vitro studies confirmed that overall expression of either ASE-GSN or wild-type GSN (WT-GSN) isoform inversely correlated with cell proliferation, whereas the high ratio of ASE-GSN to WT-GSN correlated with increased cellular invasion. Additionally, a change in expression of either isoform caused compensatory changes in expression of the other isoform. Our results suggest that the overall expression and the balance between GSN isoforms are mediating factors in proliferation, while increased overall expression of ASE-GSN is specific to cancer tissues. As a result, we propose ASE-GSN can serve not only as a biomarker of disease and disease progression, but also as a neoantigen for head and neck squamous cell carcinoma treatment, for which only a limited number of disease-specific targeted therapies currently exist.

Abstract 4474: Functional characterization of alternatively spliced GSN in head and neck cancer

PURPOSE: Analyze the functional role of alternative splicing in HPV-related (HPV+) Head and Neck Squamous Cell Carcinoma (HNSCC) biology and oncogenesis.

HPV+ HNSCC incidence is rapidly increasing, while its oncogenic mechanisms, demographic, and clinico-pathological characteristics are largely uncharacterized and discrete from those of HPV- HNSCC. Investigation into the molecular biology of HPV pathogenesis in HNSCC may help with creation of more specific clinical tools for diagnosis and treatment, which are limited and lack accuracy. Alternative Splicing Events (ASEs), post-transcriptional modifications resulting in variant transcripts leading to alternative protein isoforms, have been under-investigated as putative causes of gene expression dysregulation in HPV+ HNSCC. Using RNA-Seq data, a genome-wide ASE discovery analysis was performed on a JHU HPV+ HNSCC cohort, which has expanded HPV+ HNSCC transcriptional characterization by identifying novel ASE biomarkers implicated in carcinogenic progression. Outlier Gene Set Analysis (OGSA) was used to identify genes with high rates of ASE and results were validated in TCGA samples from seven different cancer types. To verify the functional implications of differential isoform expression, vectors for knock-in and knock-down of WT-GSN and ASE-GSN isoforms were developed to evaluate changes in cell proliferation and invasion. ASE-GSN/WT-GSN ratio outliers were identified by OGSA in tumor samples from discovery JHU HPV+ HNSCC cohort, as well as in TCGA public domain data from HNSCC, Lung Squamous Cell Carcinoma, Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma, Bladder Urothelial Carcinoma, Breast Invasive Carcinoma, and Colon Adenocarcinoma. The increased ASE-GSN/WT-GSN ratio was also observed in a cohort of HPV+ Head and Neck Cancer Cell lines. SCC61 and UM-SCC-22B HNSCC cell lines were used to evaluate the function GSN ASEs in vitro. Overall expression levels of both GSN isoforms inversely correlated with cell proliferation whereas the high ratio of ASE-GSN to WT-GSN correlated with increased cellular invasion of stroma in vitro. Additionally, a decrease or increase in expression of one isoform is seen to cause a compensatory increase or decrease in the other isoform respectively. ASE-GSN outliers correlated with HPV+ cancers indicate that expression ratio between GSN isoforms is related to tumor behavior, which is reinforced in vitro where WT-GSN is inversely correlated and ASE-GSN is directly correlated to with cell invasion. These relationships suggest that both overall expression and balance between the two GSN isoforms are mediating factors in cell death or proliferation, while shorter ASE-GSN is more likely to indicate progression to cancer. Finally, we propose a mechanism for the role of GSN isoforms in apoptosis and metastasis, in which trends in expression between WT- and ASE-GSN isoforms can alternatively affect rates of apoptosis or metastatic ability.

Citation Format: Dylan Z. Kelley, Emily L. Flam, Theresa Guo, Craig Bohrson, Michael Considine, Ludmila V. Danilova, Justin A. Bishop, Chi Zhang, Wayne M. Koch, David Sidransky, William Westra, Sarah Wheelan, Liliana Florea, Elana J. Fertig, Joseph A. Califano, Daria A. Gaykalova. Functional characterization of alternatively spliced GSN in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4474. doi:10.1158/1538-7445.AM2017-4474

Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma

Alternative splice events (ASES) are significant components of potential oncogenic pathways alterations and play a critical role in malignant cell transformation in a variety of solid and liquid tumors, including head and neck squamous cell carcinoma (HNSCC). However, high throughput analyses performed to date have not considered ASEs. Therefore, they have detected a limited number of genetic alterations for HNSCC, which incompletely describe the HNSCC specific pathway alterations. The heterogeneous nature of these alterations has made the discovery of reliable HNSCC biomarkers and therapeutic targets for this disease challenging.

We performed alternative splice events (ASEs) analysis to enhance our understanding of HNSCC biology. To define ASEs specific to HNSCC we designed a novel bioinformatics pipeline from RNA-sequencing data of HNSCC tumors and independent normal samples. Evaluating the top scoring candidates, we have found several highly promising ASE candidates, including GSN, Gelsolin, an actin-binding protein, a key regulator of actin filament assembly and disassembly.

Previously published literature proposes that GSN demonstrates tumor-suppressor properties by reducing cell proliferation in vivo and in vitro via suppression of protein kinase C (PKC, part of the PI3K pathway which is altered in HNSCC). The alternative splicing event involves an insertion of 110 bp from the 14th intron. This insertion contains a stop codon in frame, and the splice variant gives rise to a truncated (562 amino acids(aa)) protein with only 4 Gelsolin domains (instead of the full-length 731 aa protein with 6 Gelsolin domains). Using RNA-Seq data we demonstrated that 40% of tumor samples harbor the GSN-ASE. QRT-PCR confirmed that while total expression of GSN is decreased in HNSCC samples, GSN is expressed in the alternative truncated form only in HNSCC tumors and not normal tissues. Accordingly, total GSN expression is also seen to be downregulated in breast, lung and colon cancers.

Evaluation of TCGA data confirmed the pre-dominant expression of the truncated GSN isoform over the wt GSN in HNSCC, bladder urothelial carcinoma, colon adenocarcinoma, lung SCC, breast invasive carcinoma, cervical SCC and endocervical adenocarcinoma. Moreover, we confirmed that that the expression of the truncated GSN is important for the migration and invasion of the cancer cells in vitro. These data suggest that alternative splicing plays an important role in the GSN gene for multiple tumor types.

Citation Format: Daria A. Gaykalova, Dylan Kelley, Theresa Guo, Craig Bohrson, Ilse Tiscareno, Veronika Zizkova, Michael Considine, Ludmila Danilova, Emily Flam, Justin Bishop, Julie Ahn, Samantha Merritt, Marla Goldsmith, Chi Zhang, Wayne Koch, William Westra, Zubair Khan, Michael Ochs, Sarah Wheelan, Elana Fertig, Joseph Califano. The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2880.

ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells

Short telomeres induce a DNA damage response, senescence, and apoptosis, thus maintaining telomere length equilibrium is essential for cell viability. Telomerase addition of telomere repeats is tightly regulated in cells. To probe pathways that regulate telomere addition, we developed the ADDIT assay to measure new telomere addition at a single telomere in vivo. Sequence analysis showed telomerase-specific addition of repeats onto a new telomere occurred in just 48 hr. Using the ADDIT assay, we found that ATM is required for addition of new repeats onto telomeres in mouse cells. Evaluation of bulk telomeres, in both human and mouse cells, showed that blocking ATM inhibited telomere elongation. Finally, the activation of ATM through the inhibition of PARP1 resulted in increased telomere elongation, supporting the central role of the ATM pathway in regulating telomere addition. Understanding this role of ATM may yield new areas for possible therapeutic intervention in telomere-mediated disease.