Tumor Immune Evasion of HPV+ Head and Neck Squamous Cell Carcinoma

Project Overview

This project analyzes the mechanisms of tumor immune evasion in HPV+ head and neck squamous cell carcinoma (HNSCC) by studying the epigenetic downregulation of MHC-I by PRC2. The study involves performing CUT&RUN on SCC90 HPV+ HNSCC cells treated and untreated with GSK126, an FDA-approved EZH2 inhibitor.

Methods

CUT&RUN

  • Cell Line: SCC90 HPV+ HNSCC cells
  • Treatment: Untreated (DMSO) and treated with GSK126
  • Cell Number: 5 x 10^5 cells per target
  • Replicates: 2 replicates per target

Library Preparation

  • Kit: CUTANA ChIC/CUT&RUN kit (Epicypher, version 3)
  • Purification: Qubit dsDNA HS kit
  • Library Prep: CUTANA CUT&RUN Library Prep kit (Epicypher, version 1)

Sequencing

  • Platform: NovaSeq 6000 (Illumina)
  • Read Length: 2x50 bp
  • Read Depth: 8-10 million reads per library

Data Processing

  • Pipeline: nf-core/cutandrun v3.2.2
  • Alignment: Bowtie2 v2.4.4 to GRCh38 and K12-MG1655
  • Peak Calling: SEACR v1.3
  • Consensus Peaks: Merged using bedtools v2.31.0
  • Visualization: IGV desktop v2.16.1

Results

QC and Correlation Plots

Figure 1: Correlation Plot: QC Plots

Peak Analysis

Figure 2: IGV Plot of HLA-B Locus: IGV Plot HLA-B Figure 3: IGV Plot of HLA-C Locus: IGV Plot HLA-C

Differential Binding Analysis

Results from DiffBind and ChIPseeker analyses. Figure 4: MA Plot: MA Plot

Figure 5: Volcano Plot: Volcano Plot

Figure 6: Heatmap: Heatmap

Figure 7: Venn Diagram: Venn Diagram

Figure 8: Profile Plot: Profile Plot

Conclusion

Our study found accumulation of H3K27me3 at the HLA-B and HLA-C loci, as well as several other MHC-I accessory/chaperone loci that was decreased following treatment with GSK126.