Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased in recent years. RNAseq was performed for systems-based analysis of cellular pathways involved in HPV+ve OPSCCs.
Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas.
Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas.
Project description:Oropharyngeal squamous cell carcinoma (OPSCC) is diagnosed in 93,000 patients worldwide per year and 51,000 annual deaths can be attributed to this disease. OPSCCs are either human papillomavirus associated (HPV-positive) cancers or non-virally induced, primarily tobacco and alcohol associated (HPV-negative) cancers. MS analysis enabled the identification of naturally HLA-presented peptides in OPSCC tumor tissue. By comparative profiling against benign HLA ligandomic datasets, we demonstrated that tumor-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi-) personalized strategies.
Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
Project description:Human papillomavirus (HPV)-related multiphenotypic sinonasal carcinoma (HMSC) is a recently described rare tumor that is morphologically similar to high grade adenoid cystic carcinoma (ACC), but clinically distinct. We utilized single-cell RNA sequencing (scRNA-seq) to characterize transcriptional heterogeneity in a human HMSC tumor and compared it to published ACC and oropharyngeal squamous cell carcinoma (OPSCC) scRNA-seq datasets.
Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium MethylationEPIC BeadChip Kit was used to obtain DNA methylation profiles across more than 850,000 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
Project description:Oropharyngeal squamous cell carcinoma (OPSCC), a distinct head and neck cancer subtype that develops in the oropharynx, is well known to be categorized into human papillomavirus induced (HPV+) and non-HPV induced (HPV-). While HPV+ OPSCC is reported to be clinically advantageous compared to HPV- OPSCC, the heterogeneous responses in HPV+ OPSCC during immunotherapy treatment have not been well characterized at the molecular level. In this study, we assess both tumor and immune cells of the OPSCC tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq). By dissecting the transcriptome of OPSCC tumor cells, we find that cancer cell transcriptional diversity may be a strong factor in negating HPV associated clinical benefits. By assessing immune cells, we observed molecular antiviral and anti-tumor characteristics of T cells that is associated with HPV infection, and key cell-cell interaction differences among resident memory T cells (Trm), follicular helper T cells, and B cells. Importantly, we identify a novel molecular state within the HPV+ OPSCC that is distinguished by the expression KLRB1 (CD161) in the Trm that inhibits anti-tumor activity, which may further explain the heterogeneous clinical benefits of HPV+OPSCC. Association of KLRB1 expression of Trm and immunotherapy outcome was confirmed via immunofluorescence analysis, suggesting CD161 as a novel therapeutic target to improve cancer treatment of HPV+ OPSCC.
Project description:Heterogeneity in HPV status within HPV-associated oropharyngeal squamous cell carcinoma (HPV-OPSCC) has gained attention, but the origin and relevance of HPV-absent cancer cells remain unclear. Among 83 OPSCCs, including 48 HPV-OPSCCs, seven showed spatial HPV heterogeneity. Using HPV-DNA in situ hybridization, histomorphology, immunohistochemistry, and spatial transcriptomics, we revealed that HPV-absent subsets differentiate from initial HPV-positive cells, forming distinct lineages. HPV-OPSCC was associated with p16 expression, with HPV-absent clones showing robust p16 expression and poorly differentiated histology. Despite these aggressive features, prognosis was comparable to HPV-homogeneous tumors, likely due to tumor microenvironment differences. HPV-absent clones exhibited increased interferon signaling, hypoxia signaling, and cytotoxic lymphocyte infiltration, indicating a loss of antiviral immune evasion. Conversely, HPV-positive clones were linked to FGFR3 ligand-receptor signaling. This study highlights the emergence, evolution, and microenvironmental impact of HPV-absent clones in HPV-OPSCC.
