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Subtype-specific 3D genome alteration in acute myeloid leukaemia

Abstract

Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1,2,3,4,5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter–enhancer and promoter–silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.

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Fig. 1: Genome organization and compartment analysis in primary AML samples.
Fig. 2: AML and subtype-specific chromatin loops.
Fig. 3: Identification and validation of repressive loops.
Fig. 4: Identification, characterization and screening of enhancer hijacking in AML.
Fig. 5: Identification and validation of silencer hijacking in AML.
Fig. 6: Inhibition of DNA methylation restores chromatin structure and gene expression.

Data availability

The processed data from CUT&Tag, ATAC-seq, Hi-C and WGBS of primary samples and cell lines and the raw sequencing data for all cell lines have been deposited at Gene Expression Omnibus with the open session GSE152136. All processed data were generated by mapping to human reference genome GRCh38. Source data are provided with this paper.

Code availability

The code for stripe identification is available at GitHub with the following link: https://github.com/XiaoTaoWang/StripeCaller.

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Acknowledgements

F.Y. is supported by NIH grants R35GM124820, 1R01HG009906, R01HG011207, U01CA200060 and R24DK106766 (R.C.H. and F.Y.). We acknowledge the use of the Integrated Genomics Operation Core, funded by the Memorial Sloan Kettering Cancer Center Support Grant NIH P30 CA008748. This work was supported by National Cancer Institute R35 CA197594-01A1 (R.L.L.), National Cancer Institute R01 CA216421 (R.L.L.) and National Cancer Institute PS-OC U54 CA143869-05 (R.L.L). A.D.V. is supported by National Cancer Institute career development grant K08 CA215317, the William Raveis Charitable Fund Fellowship of the Damon Runyon Cancer Research Foundation (DRG 117-15) and an Evans MDS Young Investigator grant from the Edward P. Evans Foundation. T.Y. is supported by U01DA053691. The CUT&Tag reagent pA–Tn5 was provided as a gift from S. Henikoff’s Lab at Fred Hutchinson Cancer Research Center. The dCas9-UTX plasmid was provided as a gift by S. M. Offer’s Lab at Mayo Clinic.

Author information

Authors and Affiliations

Authors

Contributions

F.Y. conceived and supervised the project. J.X. and F.S. led the investigation. J.X., H.L., B.Z. and M.K. performed Hi-C, ATAC-seq, CUT&Tag, ChIP-seq, RNA-seq and 5-AZA-related experiments, and prepared DNA for WGS and WGBS. J.X. and H.L. performed CRISPR screening. J.X. performed 4C. H.L. and J.X. performed CRISPRi. M.K. and L.S. performed CRIPSR deletion. Z.Z. performed DNA FISH. Y.Y. and T.Y. supervised DNA FISH analyses. Qi Jin helped with FACS. J.H.W. performed reporter assays. H.Y. and Qiushi Jin performed DNMT TKD and HiChIP. F.S., J.X., Y.L., Y.F. and Q.W. conducted data analysis. X.W. developed the algorithm for stripe detection. Y.D., S.D., R.C.H. and J.R.B. contributed biological insights. H.Z., B.J., D.C., J.R.B., R.L.L., A.D.V. and L.C.P. provided the samples and clinical insights. J.X., F.S. and F.Y. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Hong Zheng or Feng Yue.

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Competing interests

F.Y. is a co-founder of Sariant Therapeutics, Inc. The other authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1

List of genomic experiments performed in this study.

Extended Data Fig. 2 Examples of genes with A/B compartment switch.

a and c, PC1 values and the expressions for WT1, POU2AF1, FGF13, and BCL11B genes. b, A compartment associated with higher H3K27ac and ATAC-seq signals and lower H3K27me3 intensities. Shown in figure are the ATAC-seq, CUT&Tag for H3K27ac and H3K27me3 signals at WT1 gene promoter, normalized to sequencing depths. Promoter is defined as within +/-1Kb of TSS. P value by two-sided Wilcoxon rank-sum test. PC1: A (n = 15 samples) B (n = 7 samples); H3K27ac: A (n = 15) B (n = 6); H3K27me3: A (n = 15) B (n = 6); ATAC-seq: A (n = 14) B (n = 7). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range.

Source Data

Extended Data Fig. 3 TAD boundary alteration and transcription.

a, Illustration for how alteration of TAD boundary is defined in this study. b, COSMIC cancer-related genes that are located in TADs with recurrent change of boundary. Y axis is the number of incidences across different samples. c, Differential expression analysis of genes located inside recurrently altered TADs. P value by two-sided Student t-test.

Source Data

Extended Data Fig. 4 AML-specific loop analysis.

a, Overlap of AML-specific loops with CNVs. Color scheme: neutral (blue), gain (orange), or loss (green) of copies. b, Genome-wide CNV profiles for all the 10kb bins. c, GSEA analysis for differentially expressed genes associated with AML-specific loops. P value is calculated by permutation test.

Source Data

Extended Data Fig. 5 AML-specific loops associated with sample-specific open chromatins and gene expression.

a, Hi-C maps for the MEIS1 and ERG gene regions. Left lower halves are for AML samples and the right upper halves are for HSPC and PBMC. The loops are absent in all three PBMC samples (only one is plotted) and less frequent in the four HSPC samples (only one is plotted). b-c, RNA-Seq, CUT&Tag for H3K27ac and H3K27me3, and ATAC-Seq data for regions surrounding the three genes. Purple arcs indicate chromatin loops predicted in at least two AML samples. Shown in the figure are two representative AML samples.

Extended Data Fig. 6 Analysis of promoter-silencer (P-S) loops.

a, Percentage of P-S loops among all chromatin loops in all samples. b, Size distribution of P-S loops in all samples. c, Percentage of P-S loop anchors overlapping with CTCF binding peaks. d, Normalized EZH2 CUT&Tag signals at H3K27me3 peaks in the P-S loop anchors in THP-1 cells. e, Expression of genes that are located in the P-E vs. P-S loop anchors. P value was calculated by the two-sided Kruskal-Wallis test. P-E loops (n = 31332), P-S loops (n = 7912). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. f, Expression of genes in different patient samples with different distance to the nearest non-looping H3K27me3-marked silencer. P value calculated by one-sided Wilcoxon rank-sum test. N = 3809, 4403, 3865, 3217, 2490 genes (from left to right each category). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. g. Distance distribution between the IKZF2 promoter to control or its looped silencers in Kasumi-1 (n = 112 alleles). P value by two-sided Wilcoxon rank-sum test. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range.

Source Data

Extended Data Fig. 7 Validation of a P-S loop for the RTTN gene.

a, Hi-C and H3K27me3 CUT&Tag data in AML patient sample 496 and Kasumi-1 cells, which have the P-S loop for RTTN. AML sample 018 has the same loop but with less interacting signals and almost no H3K27me3 signals at the loop anchor. The orange tracks are the 4C data for RTTN in Kasumi-1 cells. b, (Right) DNA FISH imaging to measure the distance between RTTN promoters and the looped silencers in THP-1 cells. The control is the region on the other side of the RTTN promoter, with equal linear genomic distance. (Left) distance distribution between promoter and control or its looped silencer from 144 THP-1 cells (P value = 1E-9, two-sided Wilcoxon rank-sum test). Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. c, RNA expression of RTTN across patient samples and normal controls. Normal HSPC&PBMC n = 6 samples, AML w/o P-S loop n = 13, AML with P-S loop n = 10. P value was computed by the two-sided Student’s t-test. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. d, The design of PCR for detecting CRISPR deletion of the RTTN silencer (vertical bar in the H3K27me3 track). e, Two replicates of PCR results confirming the heterozygous deletion of the RTTN silencer. The red arrow points to the amplification of the CRISPR deletion junction (~700bp), and the blue arrow points to the wildtype band (~300bp). f. Sanger sequencing confirmed the CRISPR deletion of the silencer. g, qPCR results of RTTN expression in the clone with this heterozygous deletion vs. control group. The control group is other clones that underwent the same CRISPR system treatment without deletion (n = 3 technical replicates in 2 biological replicates). P value by two-sided Student’s t-test. Data show mean ± s.e.m. h, CCK-8 assay results for proliferation of Kasumi-1 cells with the RTTN silencer deleted vs. both the wildtype and the CRISPR control cells in panel g (n = 3 biological replicates). i, Stereomicroscope images of CFA cells on day 12 at 7.5X zoom. CFA was performed in n = 3 replicates. j, Size (pixel) distribution of WT colonies (n = 40) and the colonies with RTTN silencer deleted (n = 35), measured by imageJ. P value calculated by two-sided Wilcoxon rank-sum test. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range.

Source Data

Extended Data Fig. 8 Analysis of chromatin stripes.

a, Hi-C maps for the MYC gene regions. Left lower panels are for AML samples and the right upper panels are for HSPC and PBMC. Black arrow marks a stripe. b, RNA-Seq, CUT&Tag for H3K27ac and H3K27me3, and ATAC-Seq data for regions surrounding the MYC genes. c, Classification of stripes based on whether the anchors contain gene promoters and the stripe zones contain enhancers (H3K27ac) or silencer marks (H3K27me3). d, In each patient samples, genes in enhancer stripes have higher expression than genes in silencer stripes. P-value by two-sided Kruskal–Wallis test. P-E stripes n = 4310, P-S stripes n = 2518. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. e. For each gene involved with a P-E stripe, samples were grouped into two categories: samples with P-E stripe, and samples with neither P-E nor P-S stripe for this gene. So was for P-S stripe analysis. Then the average gene expression (TPM) within each category was calculated. P value by two-sided Kruskal-Wallis test. Left: n = 461 genes; Right: n = 415 genes. Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range.

Source Data

Extended Data Fig. 9 Detection and analysis of SV-induced neo-loops.

a, Detection of SVs in AML samples from Hi-C data, marked by the black arrow in Hi-C maps. Left: inv(16). Middle: t(6;9). Right: t(8;13). b, Distribution of genomic distances between translocations/deletions to the nearest cancer-related genes (COSMIC database). Expected value is calculated by random permutation of the SVs in the genome for 1000 times. P value is calculated by two sample Kolmogorov-Smirnov test. TL: translocation. DEL: deletion. c, An example of reconstructed Hi-C maps surrounding the SV breakpoint between chr7 and chr11 in the AML sample 270. We also showed the inter-chromosomal Hi-C map in the HSPC 213, where there is no visible inter-chromosomal interactions. The orientation of the SV is marked by the arrows, which always point from 5’ to 3’. The neo-loop for CDK5 is circled. Above the Hi-C: predicted 3D structure for the region in normal and AML sample visualized by PyMOL. d, Recurrent enhancer hijacking involving the CBL gene and enhancers. e, RNA expression of the CBL gene in all samples.

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Extended Data Fig. 10 Enhancer hijacking analysis and validation.

a, Motif enrichment analysis for all hijacked enhancers in AML. The number in each box is the P-value (–log10) calculated by binomial test. b, The list of hijacked enhancers being validated, the corresponding sgRNA, and their targeted genes over SV. c, H3K27ac at the sgRNA-targeted loci and the NSMCE3 gene promoter. d, qPCR relative gene expression in THP-1 cells expressing dCas9-KRAB-MeCP2 (n = 3 technical replicates in 2 biological replicates). P value by two-sided Students’ t-test. Data show mean ± s.e.m. e, qPCR results of the targeted gene expression in Kasumi-1 cells with repressing the hijacked enhancers ((n = 3 technical replicates in 2 biological replicates)). P value by two-sided Student’s t test. Data show mean ± s.e.m.

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Extended Data Fig. 11 Aberrant DNA methylation in AML is associated with changed CTCF binding and chromatin structures.

a, Genome-wide CG methylation level in HSPC, PBMC, and AML samples. Data for HSPC* was downloaded from Tovy et al., Cell Stem Cell, 2020. b, CG methylation levels at TSS regions (upper) and gene bodies (lower) in A and B compartment. (Upper) A (n = 531,112 TSS) B (n = 204,365 TSS), (Lower) A (n = 340,385 genes) B (156,852 genes). Box plot: middle line denotes median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range of the first and third quartile. c, (Left) Heatmaps of CTCF CUT&Tag signals in AML samples ranked by normalized peak intensity. (Right) Methylation levels surrounding the CTCF binding sites from the same samples. d, Heatmaps showing dynamic CTCF binding sites and methylation levels in AML 424 vs. HSPC. (Right) Hypermethylated sites in AML 424 vs. HSPC that also overlapped with CTCF binding sites in HSPC. Hypermethylation is defined as CpG methylation levels significantly different between two samples (beta-binomial distribution p-value<0.01) and at least 0.3 higher in AML sample. (Left) CTCF signals at the dynamic methylated regions. e, A model for gain of loops as a result of loop extrusion over loss of CTCF binding. f, For AML 424 and HSPC 213, we separately aggregated their Hi-C plots that are centered at the 142 reduced CTCF binding sites of AML 424 associated with hypermethylation. The two aggregated plots were then normalized by total contacts and distance, and the difference is calculated as log2 of fold change. The diamond-shaped region between the two dashed lines resided the interactions across the lost CTCF sites. g, Differential CTCF binding and chromatin loops. Blue vertical bar marks a differential CTCF binding site that was absent in four AML samples. The CTCF binding motifs were also hypermethylated in the AML samples. We observed additional loops across the lost CTCF binding sites in these AML samples.

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Extended Data Fig. 12 Effect of 5-AZA treatment on DNA methylation and cell phenotypes.

a, CCK-8 assay started with n = 3 biological replicates of 1,000 cells per well in 96-well plate. The assay completed on day 8 as the DMSO group grow confluent. Data show mean ± s.e.m. MW: molecular weight. b, Western Blot results for Caspase-3. AA2 is Apoptosis Activator 2 (TOCRIS 2098). The experiments were independently repeated twice with similar results. c, Western Blot for yH2AX. UV light condition is detailed in method. The experiments were independently repeated twice with similar results. d, Flow cytometry result for cells treated with either DMSO or 5-AZA 0.5μM. e, Flow cytometry results for cells treated with 1μM, 2μM, 4μM, and 8μM 5-AZA for 2 days.

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Extended Data Fig. 13 Impact of 5-AZA treatment on chromatin structure.

a, Global CG methylation levels of U937 under DMSO or 5-AZA treatment. b, A snapshot of DNA methylation levels across a genomic region. c-d, DNA methylation levels at CpGi, CpG shores (<2Kb), CpG shelves (2Kb-4Kb), open sea (rest of genome), and CTCF binding sites under 12-day DMSO or 0.5μM 5-AZA treatment. DMSO: n = 2,691,094 CpG types, 5-AZA n = 2,669,959 CpG types. CTCF binding sites were defined from HSPC cells. N = 10,960 CTCF sites. P value by two-sided Wilcoxon rank-sum test. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range. e, Enrichment of CpGi and open sea at each type of switching compartment. P value by two-sided Wilcoxon rank-sum test. From left to right for both CpGi and Open sea: n = 808, n = 372, n = 636, n = 338; Box plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. f. Methylation levels for each type of switching compartment at CpGi (upper) and open sea (lower). From left to right: CpGi panel: n = 20,566, n = 450, n = 4,651, n = 910; Open sea panel: n = 591, n = 731, n = 4,531, n = 1,398. P value by two-sided Wilcoxon rank-sum test. AB: A in DMSO group and B in 5-AZA group. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range. g, CpGi at one or both anchors of two types of loops under 5-Aza treatment. h, Methylation levels for two types of loops at CpGi and open sea. From left to right: CpGi panel: n = 2,871, n = 596; Open sea panel: n = 117,177, n = 20,499. P value by two-sided Wilcoxon rank-sum test. Violin plot: middle line denotes the median, top/bottom of boxes denotes first/third quartiles and boundary extend to 1.5 times the interquartile range.

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Xu, J., Song, F., Lyu, H. et al. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 611, 387–398 (2022). https://doi.org/10.1038/s41586-022-05365-x

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