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

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Nagarajan D, Parracho RT, Corujo D, Xie M, Kutkaite G, Olsen TK, Rúbies Bedós M, Salehi M, Baryawno N, Menden MP, Chen X, Buschbeck M, Mao Y

J. Clin. Invest. - (-) - [2024-09-10; online 2024-09-10]

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 neuroblastoma patients 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 sequencing 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 multi-omics approach, we uncover 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.

CRISPR Functional Genomics [Service]

PubMed 39255035

DOI 10.1172/JCI175310

Crossref 10.1172/JCI175310

pii: 175310