Contributions
Abstract: EP372
Type: E-Poster Presentation
Session title: Acute myeloid leukemia - Biology & Translational Research
Background
Changes in 3D chromatin organization like enhancer hijacking are believed to the driver for disease development like leukemia. Here we performed high-resolution HiC assays on primary acute myeloid leukemia (AML) samples and cell lines to dissect the abnormal 3D chromatin organization in AML. We have recently generated a high-resolution map for normal human hematopoietic stem cells (HSC) (Zhang et al. Mole Cell. 2020).
Aims
To dissect the pathogenic alteration in 3D genomics of acute meyloid leukemia
Methods
We use in situ HiC to generate the high resolution HiC contact map. Our data set covers 5 AML samples and 3 AML cell lines. This dataset includes the common genetic abnormalities in AML: MLL-rearrangement, NPM1 mutation, RUNX1 mutation, and IDH1/TET2 mutations (Figure 1A,B).
Results
In comparison with the HSC 3D chromatin organization, we found TADs and loops are very stable in both primary leukemia samples and cell lines. Less than 5% of all TADs in HSC without disruption of gene expression for genes located in the fused TAD. Interestingly, in TET2 or IDH1 mutated AML, two-fold more TAD fusion events occurred in comparison with RUNX1 and MLL-r leukemia, with a hypermethylation on the TAD fusion break point regions.
Compared with normal HSC, we found in AML, the AML-specific H3K27ac marked regions form leukemia specific loops and transcription stripes in both cell lines and primary samples. Particularly in MLL-r primary leukemias, we found broad H3K27ac covered, hyperacetylated domains (10kb to 200kb). 22 such hyperacetylated domains were identified and associated with leukemogenic genes such as SATB1, ZEB2 and HOXA. All these domains formed distinct 3D micro-TAD in the MLL-r primary leukemia in comparison with the HSPC, and CTCFs are not located at the border of these domains. Taken together, suggest active leukemia specific transcription created new 3D genomic interactions which is independent of cohesion-CTCF mediated loop extrusion. Particularly, we found the driving oncogenic transcriptional factor HOXA9 and MEIS1 is driving the leukemia specific 3D genomic interactions in MLL-AF9 and NPM1 mutant leukemias .
We previously found in HSC, the Polycomb marked DNA methylation Canyons (DMC) form multi-Mb size long-range interactions. DMC interactions in general decrease in primary AMLs. AMLs with IDH1 or TET2 mutations shows the biggest reduction in DMC interactions. Hypermethylation in the DMCs is observed in the all AML samples, but IDH1 and TET2 mutated AML shows the biggest reduction in the H3K27me3 enrichment in DMC regions, suggesting the level of H3K27me3 enrichment is directly correlated with the strength of DMCs. Remarkably, we found some DMCs switched to active state with gain of active chromatin market H3K27ac. Particularly, two Iroquois homeobox genes, which lies in proximity on chromosome 16 - IRX3 and IRX5 are activated in NPM1c leukemia. We found that IRX3 and IRX5 form the long-range stripe interactions with FTO intron enhancer as in the muscle and brain. Further test shows IRX3 and IRX5 is essential for the leukemia growth and the expression is directly maintained by NPM1c in a NPM1c targeted degradation system.
Conclusion
In summary, we have found in AML, specific 3D genomics interactions associated with leukemia specific transcription is established de novo. Particularly, we discovered the DNA methylation Canyon in AML switch from polycomb repressed state to activation state by direct activation of NPM1c.
Keyword(s):
Abstract: EP372
Type: E-Poster Presentation
Session title: Acute myeloid leukemia - Biology & Translational Research
Background
Changes in 3D chromatin organization like enhancer hijacking are believed to the driver for disease development like leukemia. Here we performed high-resolution HiC assays on primary acute myeloid leukemia (AML) samples and cell lines to dissect the abnormal 3D chromatin organization in AML. We have recently generated a high-resolution map for normal human hematopoietic stem cells (HSC) (Zhang et al. Mole Cell. 2020).
Aims
To dissect the pathogenic alteration in 3D genomics of acute meyloid leukemia
Methods
We use in situ HiC to generate the high resolution HiC contact map. Our data set covers 5 AML samples and 3 AML cell lines. This dataset includes the common genetic abnormalities in AML: MLL-rearrangement, NPM1 mutation, RUNX1 mutation, and IDH1/TET2 mutations (Figure 1A,B).
Results
In comparison with the HSC 3D chromatin organization, we found TADs and loops are very stable in both primary leukemia samples and cell lines. Less than 5% of all TADs in HSC without disruption of gene expression for genes located in the fused TAD. Interestingly, in TET2 or IDH1 mutated AML, two-fold more TAD fusion events occurred in comparison with RUNX1 and MLL-r leukemia, with a hypermethylation on the TAD fusion break point regions.
Compared with normal HSC, we found in AML, the AML-specific H3K27ac marked regions form leukemia specific loops and transcription stripes in both cell lines and primary samples. Particularly in MLL-r primary leukemias, we found broad H3K27ac covered, hyperacetylated domains (10kb to 200kb). 22 such hyperacetylated domains were identified and associated with leukemogenic genes such as SATB1, ZEB2 and HOXA. All these domains formed distinct 3D micro-TAD in the MLL-r primary leukemia in comparison with the HSPC, and CTCFs are not located at the border of these domains. Taken together, suggest active leukemia specific transcription created new 3D genomic interactions which is independent of cohesion-CTCF mediated loop extrusion. Particularly, we found the driving oncogenic transcriptional factor HOXA9 and MEIS1 is driving the leukemia specific 3D genomic interactions in MLL-AF9 and NPM1 mutant leukemias .
We previously found in HSC, the Polycomb marked DNA methylation Canyons (DMC) form multi-Mb size long-range interactions. DMC interactions in general decrease in primary AMLs. AMLs with IDH1 or TET2 mutations shows the biggest reduction in DMC interactions. Hypermethylation in the DMCs is observed in the all AML samples, but IDH1 and TET2 mutated AML shows the biggest reduction in the H3K27me3 enrichment in DMC regions, suggesting the level of H3K27me3 enrichment is directly correlated with the strength of DMCs. Remarkably, we found some DMCs switched to active state with gain of active chromatin market H3K27ac. Particularly, two Iroquois homeobox genes, which lies in proximity on chromosome 16 - IRX3 and IRX5 are activated in NPM1c leukemia. We found that IRX3 and IRX5 form the long-range stripe interactions with FTO intron enhancer as in the muscle and brain. Further test shows IRX3 and IRX5 is essential for the leukemia growth and the expression is directly maintained by NPM1c in a NPM1c targeted degradation system.
Conclusion
In summary, we have found in AML, specific 3D genomics interactions associated with leukemia specific transcription is established de novo. Particularly, we discovered the DNA methylation Canyon in AML switch from polycomb repressed state to activation state by direct activation of NPM1c.
Keyword(s):