Abstract A094: Single-cell Transcriptomics Unveils Novel Regulators of MHC Expression: Implications for Cancer Immunotherapy

Abstract Background: Major histocompatibility complex (MHC) genes are critical for the adaptive immune system, enabling T-cells to detect and eliminate cancer cells. Many cancers evade immune surveillance by altering MHC expression, leading to resistance to immune checkpoint blockade (ICB) therapy. Understanding MHC regulation in normal and cancerous states is essential for developing effective immunotherapies. Previous studies using bulk RNA-sequencing failed to measure cancer cell-specific MHC expression accurately. This study aims to decode MHC transcriptional regulation in healthy tissues and cancers using single-cell RNA-seq (scRNA-seq) datasets and targeted CRISPR screens. Methods: We utilized a large-scale scRNA-seq dataset encompassing 18 tissues and 124 epithelial cell types to study MHC class I (MHCI) and class II (MHCII) regulation at baseline. After re-clustering and annotation, we investigated MHC expression across various cell types and tissues, quantifying heterogeneity using the Gini coefficient. We employed a master regulator inference approach with uni- and multi-regression models to identify transcription factors (TFs) predictive of MHC expression. To investigate MHC dysregulation in cancer, we curated 43 scRNA-seq datasets across 20 cancer types and 538 patients. Results: We observed an ∼8-fold range in MHCI expression across normal epithelial cell types, with notable MHCII expression in prostate club cells and cholangiocytes of the liver. Our approach nominated 104 TFs for MHCI and 107 for MHCII, including novel regulators like YBX1 and XBP1. In our pan-cancer analysis, we found widespread repression of MHC genes, with significant heterogeneity in MHCII expression among colon cancer patients correlating with mismatch repair deficiency. In prostate cancer, MYC-mediated pathways led to MHCI suppression, revealing a novel immune evasion mechanism. In an ICB cohort, TFs such as XBP1 and SP100 were strong predictors of patient survival. This work has resulted in a data descriptor to make single-cell ICB data accessible. Conclusion: Our study provides a comprehensive evaluation of MHC expression across 124 cell types and 20 cancers, identifying TFs predictive of MHCI and MHCII expression. By uncovering novel regulatory mechanisms and potential immune evasion strategies, this research contributes valuable insights into MHC regulation in normal and cancerous tissues. The identification of YBX1 and XBP1 as potential regulators opens new avenues for targeted therapies. The correlation between MHCII upregulation and mismatch repair deficiency suggests a potential biomarker for immunotherapy response. The discovery of MYC-mediated MHCI suppression provides a new target for enhancing immune recognition. These findings have important implications for understanding cancer immune evasion and may inform the development of more effective immunotherapies and predictive biomarkers for ICB response. Future work will focus on experimental validation of these computational findings and exploring their clinical applications in cancer immunotherapy. Citation Format: Mahnoor Gondal, Yi Bao, Rahul Mannan, Jing Hu, Arul Chinnaiyan, Marcin Cieslik. Single-cell Transcriptomics Unveils Novel Regulators of MHC Expression: Implications for Cancer Immunotherapy [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr A094.