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

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Figure 4

Epigenetic and translational profiling of H2afy-deficient NB cells.

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Epigenetic and translational profiling of H2afy-deficient NB cells. The ...
The regulatory role of H2AY protein in control or KO 9464D cells was mapped using CUT&RUN. (A) Heatmap and mean profile visualization of the H2AFY CUT&RUN signal in 9464D cells across enriched domains was identified with epic2, using KO cells as the negative control. Every region was scaled to the same size and extended +/– 3 kb in each side. A nontargeting IgG was used as a negative control. The average signal of 2 experimental replicates is represented. (B) Number of overlapping differential ATAC-Seq peaks with H2AFY domains from the CUT&RUN dataset is shown. * P < 0.05, permutation test. (C) Genomic annotation distribution of downregulated ATAC-Seq peaks classified by their overlap with H2AFY-enriched domains in CUT&RUN. The translational landscape in control or H2AFY-deficient 9464D cells was mapped using label-free proteomics. (D) Differentially expressed proteins were visualized in a volcano plot using Log2 FC and Log10 P values. (E) The lack of H2AFY protein was confirmed using proteomics. Pathway analysis according to the (F) upregulated proteins or downregulated proteins in KO cells compared with control cells (FDR < 0.05 and Log2FC > 0.5).