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Medulloblastoma (MB) is the most common malignant childhood brain tumor1,2, yet the origin of the most aggressive subgroup-3 form remains elusive, impeding development of effective targeted treatments. Previous analyses of mouse cerebella3,4or human counterparts from frozen tissue nuclei5have not fully defined the compositional heterogeneity of MBs. Here, we undertook an unprecedented single-cell profiling of freshly-isolated human fetal cerebella to establish a reference map delineating hierarchical cellular states in MBs. We identified a unique transitional cerebellar progenitor connecting neural stem cells to neuronal lineages in developing fetal cerebella. Intersectional analysis revealed that the transitional progenitors were enriched in aggressive MB subgroups, including group-3 and metastatic tumors. Single-cell multi-omics revealed underlying regulatory networks in the transitional progenitor populations, including transcriptional determinants HNRNPH1 and SOX11, which are correlated with clinical prognosis in group-3 MBs. Genomic and Hi-C profiling identifiedde novolong-range chromatin-loops juxtaposing HNRNPH1/SOX11-targeted super-enhancers tocis-regulatory elements of MYC, an oncogenic driver for group-3 MBs. Targeting the transitional progenitor regulators inhibited MYC expression and MYC-driven group-3 MB growth. Our integrated single-cell atlases of human fetal cerebella and MBs reveal potential cell populations predisposed to transformation and regulatory circuitries underlying tumor cell states and oncogenesis, highlighting hitherto unrecognized transitional progenitor intermediates predictive of disease prognosis and potential therapeutic vulnerabilities.

Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

Cis-regulatory elements (CREs) play instrumental roles in the regulation of mammalian gene expression. Sets of transcriptional factors bring together multiple CREs, which can be up to megabases away, to initiate and maintain the gene expression. How to measure the activity of CREs and their coordination with the genetic variants over large genomic distances to regulate gene expression is the central question for regulatory genomics, which is still limited by the current sequencing approaches. We report a method, TAGMe-seq, which simultaneously captures the single nucleotide polymorphisms (SNPs), chromosome conformation, DNA methylation, and GpC methyltransferase footprints from a single molecule, together with transcriptome in the same assay.To demonstrate the performance of TAGMe-seq, we applied it to the IMR-90 and GM12878 cell lines, both of which have been comprehensively profiled publically. TAGMe-seq showed high concordances with the state-of-art mono-omics assays across all the molecular measurements at the same cell types. We next asked if the genomic regions linearly separated but positioned proximity in space would have coordinated footprint status. We analyzed the GCH (H=A, C, or T) methyltransferase footprint on TAGMe-seq reads separated in chromatin loop anchors. Indeed, the GCH methyltransferase footprint in TAGMe-seq read pairs mapping to separated loop anchors showed a significantly higher correlation than that in the shuffled read pairs from the same genomic regions. To further demonstrate the utility of TAGMe-seq, we utilized it to analyze the long-range (>1kb) allele-specific GpC methyltransferase footprint. We separated TAGMe-seq reads into two groups by their parent-of-origin at the heterozygous SNPs (SNP anchors). Naturally, the other ends of the read pairs were also separated into two alleles, even though they are not overlapped with the SNPs and mapped over large genomic distances (non-SNP anchors). Thus, we are able to analyze the long-range allele-specific GCH methyltransferase footprint. We identified three groups of allele-specific footprint loci based on their differences of GCH accessibility between the two alleles at both anchors, or only at SNP anchors, or only at non-SNP anchors, which showed distinct enrichment levels of TF binding. Overall, combining multiple assays in TAGMe-seq allowed us to uncover the coordinated GpC methyltransferase footprint and long-range allele-specific footprint at genomic regions that are far away in linear DNA sequences but spatially close in the nucleus, which will eventually pave the road to dissect the mechanisms of gene-regulatory aberrations in complex diseases, such as cancer. Citation Format: Hailu Fu, Haizi Zheng, Louis J. Muglia, Li Wang, Yaping Liu. Simultaneous profiling of genetic variants, 3D genome, GpC methyltransferase footprints, DNA methylation, and transcriptome in a single assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5797.