Abstract 2466: tRNA-derived fragments as immunotherapy response targets in head and neck squamous cell carcinoma
Authors: Rishabh Yalamarty, Daniel John, Annie Do, Tianyi Chen, Megan Ngo, Pranava Gande, Matthew Uzelac, Wei Tse Li, Weg M. Ongkeko
Journal: Cancer Research (2024)

Abstract Background: Despite significant advances in immunotherapy-based treatment options for Head and Neck Squamous Cell Carcinoma (HNSCC), patient prognosis and survival remains poor. To enhance response to immune-based therapies, specific targeting of immunomodulatory pathways has been investigated through co-stimulatory gene targets, the microbiome, and more. An emerging biomolecule is Transfer RNAs (tRNAs), which are a class of RNAs that transport amino acids from the cytoplasm to ribosomes, and synthesize new proteins encoded by mRNA transcripts. tRNA-derived fragments (tRFs) are a category of cleaved, mature tRNA that participate in post-transcriptional regulation and have been implicated in the modulation of cancer and other immune-associated diseases. While tRFs are primarily implicated in diagnostic signatures for various cancers, few studies have investigated their role in modulating the immunotherapy-based response in HNSCC. In this study, we characterized the role of tRFs in modulating immunotherapy gene targets pertinent to HNSCC. Methods: We extracted tRF read counts from MINTbase 2.0 for 455 primary HNSCC tumor samples and 44 adjacent normals. Differential expression analysis was first performed to identify tRFs implicated in HNSCC tumors, with respect to adjacent normal tissue. Next, these tRFs were associated with immunotherapy target genes and response markers with Spearman’s correlation. Further characterization of these tRFs was performed by correlating their abundance to infiltrating immune cells, pathway enrichment of immunotherapy targets, and clinical variables. Results: Significant differential expression of tRFs were found between HNSCC primary tumor samples and adjacent normal tissue, including 7 tRFs (FDR &amp;lt; 0.05, |log fold change| &amp;gt; 0.5). All were enriched in normal samples. AlaCGC5tRF appeared to be an important regulator of immunotherapy target genes through increased co-expression of PTPN11, STAT3, and PTEN (p-value &amp;lt; 0.05, R &amp;gt; 0) and decreased co-expression of CD58 and TNFRSF14 (p-value &amp;lt; 0.05, R &amp;lt; 0). Immune Checkpoint Inhibitor (ICI) genes were significantly correlated with several tRFs. Among several pertinent tRF markers, AlaCGC5tRF was strongly associated with negatively correlated with infiltrating activated NK cells naïve CD4 T cells (p-value &amp;lt; 0.05, R &amp;lt; 0). Conclusion: Our study is the most comprehensive to date to characterize the role of tRF elements in modulating HNSCC immunotherapy targets. We found several potential tRF biomarkers that may be indicative of enhanced immunotherapy treatment susceptibility, including AlaCGC5tRF and ArgTCT3tRf. Further studies are needed to investigate how these tRFs may be targeted alongside immunotherapies to enhance response to treatment. Citation Format: Rishabh Yalamarty, Daniel John, Annie Do, Tianyi Chen, Megan Ngo, Pranava Gande, Matthew Uzelac, Wei Tse Li, Weg M. Ongkeko. tRNA-derived fragments as immunotherapy response targets in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2466.