Extended Data Fig. 1: Regulation of B7-H3 expression in ATRT and during normal brain development.
a, Flow cytometric analysis of B7-H3 expression on ATRT cell lines. Representative of two independent experiments is shown b, Quantification of B7-H3 molecules per cell on ATRT cell lines using flow cytometry (TYR n = 3, SHH n = 3, MYC n = 3; TYR vs. SHH p = 0.700; TYR vs. MYC p = 0.400; SHH vs MYC p = 0.200) (Mann-Whitney test, two-tailed). c, B7-H3 mRNA upon SMARCB1 re-expression from datamining of Chauvin et al (GSE98277 Cell Rep1017) published inducible SMARCB1 system in a SMARCB1-deficient rhabdoid cell line (n = 3 for all time points) 0 days vs. 2 days **p = 0.007; 0 days vs. 4 days *p = 0.011; 0 days vs. 7 days *p = 0.012; 0 days vs. 14 days **p = 0.007) (unpaired t-test, two-tailed). d, ChipSeq H3K27Ac data of the promoter region of B7-H3 in primary ATRT tumors. e, ChipSeq SMARCA4 data at the promoter region of B7-H3 in primary ATRT tumors f, RT-qPCR analysis of B7-H3 and SMARCA4 mRNA expression levels in SMARCB1-deficient ATRT cell lines (BT12 and BT16) five days after shRNA SMARCA4 knock down (k.d.) with two different short hairpins. Graph represents ΔΔCt relative to cells transduced with empty vector. Triplicates were run in each experiment. Representative results of two independent experiments is shown g, Correlation of normalized SMARCA4 and normalized B7-H3 expression from primary ATRT tumors (GSE70678) (n = 49) (r = 0.32, p = 0.026) (Pearson correlation, two-sided) h, Correlation of mRNA expression of SMARCA4 and B7-H3 during normal brain development (prenatal n = 237; pediatric n = 178; adult n = 109) (r = 0.86; p = <1x10-15) (Pearson correlation, two-sided). (i) mRNA expression levels of miR29c during and after normal brain development (prenatal n = 237; pediatric n = 178; adult n = 109). j, miR29 nanostring counts in ATRT cells lines and mature and immature neurons. k, ChipSeq H3K27Ac data around miR29 locus in primary ATRT tumors. All data are means ± s.d.
