Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma
Divya Nagarajan, … , Marcus Buschbeck, Yumeng Mao
Divya Nagarajan, … , Marcus Buschbeck, Yumeng Mao
Published September 10, 2024
Citation Information: J Clin Invest. 2024;134(21):e175310. https://doi.org/10.1172/JCI175310.
View: Text | PDF
Research Article Immunology Oncology

Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma

Abstract

Childhood neuroblastoma with MYCN amplification is classified as high risk and often relapses after intensive treatments. Immune checkpoint blockade therapy against the PD-1/L1 axis shows limited efficacy in patients with neuroblastoma, and the cancer intrinsic immune regulatory network is poorly understood. Here, we leverage genome-wide CRISPR/Cas9 screens and identify H2AFY as a resistance gene to the clinically approved PD-1 blocking antibody nivolumab. Analysis of single-cell RNA-Seq datasets reveals that H2AFY mRNA is enriched in adrenergic cancer cells and is associated with worse patient survival. Genetic deletion of H2afy in MYCN-driven neuroblastoma cells reverts in vivo resistance to PD-1 blockade by eliciting activation of the adaptive and innate immunity. Mapping of the epigenetic and translational landscape demonstrates that H2afy deletion promotes cell transition to a mesenchymal-like state. With a multiomics approach, we uncovered H2AFY-associated genes that are functionally relevant and prognostic in patients. Altogether, our study elucidates the role of H2AFY as an epigenetic gatekeeper for cell states and immunogenicity in high-risk neuroblastoma.

Authors

Divya Nagarajan, Rebeca T. Parracho, David Corujo, Minglu Xie, Ginte Kutkaite, Thale K. Olsen, Marta Rubies Bedos, Maede Salehi, Ninib Baryawno, Michael P. Menden, Xingqi Chen, Marcus Buschbeck, Yumeng Mao

×

Figure 2

Genome-wide CRISPR/Cas9 screens identified H2AFY as a resistance gene to nivolumab in human NB cells.

Options: View larger image (or click on image) Download as PowerPoint
Genome-wide CRISPR/Cas9 screens identified H2AFY as a resistance gene to...
(A) Schematic illustration of the setup of CRISPR screens using an IMR32/lymphocyte coculture. (B) Culture supernatants were collected from the flasks at the end of the CRISPR screen using donor 2. Levels of soluble IFNG and granzyme B were quantified using ELISA. (C) Venn diagram to illustrate the top and commonly depleted genes from the screens when comparing cocultures treated with or without nivolumab. (D) Performance of the 4 individual gRNAs against the top commonly depleted genes. (E) Functional enrichment analysis to capture pathways represented by the top depleted genes in the CRISPR screens. (F) Ranking of known immune resistance genes and H2AFY in the genome-wide CRISPR screen performed with the high E:T ratio, when comparing nivolumab treated and nontreated cocultures. (G) Detection of the H2AFY protein was performed simultaneously as the detection of MYCN using Western blotting in a panel of human NB cell lines. The GAPDH bands were identical to the ones in Figure 1A. Representative blot from 2 biological repeats, unpaired 2-tailed t test. ****P < 0.0001.