Neoantigen Evolution in Head and Neck Tumors

The aim of this exploratory study was to characterize the genomic and neoantigen changes in 23 paired primary and recurrent head and neck cell squamous-cell carcinomas.

True color X-Ray film of neck - front and side
True color X-Ray film of neck – front and side
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Head and neck cancer is a group of various tumors located in the oral cavity, oropharynx, larynx, and hypopharynx. Head and neck cell squamous-cell carcinomas (HNSCC) often result from tobacco use or human papillomavirus (HPV+) infection. In locally advanced HNSCC, the current therapies used are often combined surgery, radiotherapy, and chemotherapy. As HNSCC advances, mutational burden increases and, despite the use of traditional treatments, up to 50% of patients still relapse with HNSCC. 

For patients with relapsed or metastatic HNSCC, current therapies include immunotherapy, chemotherapy, or cetuximab. The FDA has also approved a relatively new immune checkpoint inhibitor therapy. The efficacy of this new therapy suggests that the immune system may play an important anti-tumor role in HNSCC. 

Researchers from Washington University in St. Louis, Columbia University, St. Louis Children’s Hospital, and Siteman Cancer Center conducted a study to characterize the genomic and neoantigen changes in 23 paired primary and recurrent HNSCC tumors. Their study, titled, “Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma,” was chosen as the cover paper for Oncotarget’s Volume 12, Issue #6.

“Prior work has characterized changes in the mutation burden between primary and recurrent tumors; however, little work has characterized the changes in neoantigen evolution.”

The Study

“Twenty-three biopsies from patients originally diagnosed with locally advanced disease were identified from the Washington University tumor bank.”

Of the 23 patients in this study, 17 were male and 14 were tobacco smokers. The distribution of primary tumor location was nine in the oral cavity, seven in the oropharynx, six in the larynx, and one in the hypopharynx. The researchers note that all seven patients with an oropharyngeal primary tumor were HPV+. All 23 patients received some combination of traditional treatment.

“To understand the recurrent mutation effect between primary and recurrent/metastatic tumors, we extract recurrently mutated genes (>1 sample mutated gene) from primary and recurrent/metastatic samples, separately.”

The team sequenced blood samples for germline WES data and used four somatic mutation tools and a bam-readcount tool. After conducting RNA sequencing, they used Kallisto to predict gene expression in 16 primary tumors and 15 recurrent/metastatic tumors. A general trend showed that more mutations were within recurrent/metastatic tumors than in primary tumors. They performed KEGG pathways analysis to determine whether mutations occurred in pathways related to metastasis.

“Notably, ECM-receptor interaction pathway was extremely significant in recurrent/metastatic samples meaning that genes related to this pathway are more highly mutated than other pathway mutations in recurrent/metastatic samples.”

The TP53 gene was found to be the highest mutated driver gene in both sample groups, and the researchers identified BRCA1 and NOTCH1 as highly mutated driver genes in primary tumor samples. In recurrent or metastatic tumors, PIK3CA, ARID1A, RASA1, TSC2, and ERBB4 were mutated higher than in primary tumor samples.

To determine the infiltration of immune cells in primary tumors versus recurrent/metastatic tumors, the team performed immunohistochemistry. No significant difference in CD3+ cells, activated T cells, cytotoxic T cells, or  CD3+ FOXP3+ cells was found. A significant increase of PD-L1 was found in recurrent/metastatic tumors. They then examined the immune checkpoint molecules and found a decrease in the expression of PDCD1 and CTLA4, with PDCD1 significantly decreased.

“We next sought to determine if genes containing neoantigens were shared between patients. Most neoantigens were unique to an individual tumor.”

In order to predict neoantigens among 46 tumor samples, this team utilized OptiType and MuPeXI to define the candidate neoantigens. Their analysis identified multiple patients with neoantigens in shared genes. Most patients had unique neoantigens based on the individual tumor type, however, five genes with neoantigens were shared between four or five patients. They found that compared to patients without them, patients that share these genes tend to have more neoantigens and increased duration of survival with HNSCC.

“These patients have increased total neoantigens, and a trend toward increased duration of survival with disease, infiltration of CD8 cells, and CTL activity. This suggests HNSCC neoantigens can stimulate an anti-tumor immune response.”


The researchers explained that while there is considerably more work needed in order to expand on their results from this small sample, having observed that five patients have neoantigens in shared genes is very significant.

“This raises the possibility that the presentation of certain neoantigens are important for control of tumor growth. This small exploratory study will provide the justification for a larger study of neoantigens in HNSCC.”

Click here to read the full scientific study, published in Oncotarget.

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