Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML
Zuzana Tothova, … , Job Dekker, Benjamin L. Ebert
Zuzana Tothova, … , Job Dekker, Benjamin L. Ebert
Published December 22, 2020
Citation Information: JCI Insight. 2021;6(3):e142149. https://doi.org/10.1172/jci.insight.142149.
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Research Article Hematology Oncology

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

Abstract

The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of stromal antigen 2–mutant (STAG2-mutant) AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to poly(ADP-ribose) polymerase (PARP) inhibition. We developed a mouse model of MDS in which Stag2 mutations arose as clonal secondary lesions in the background of clonal hematopoiesis driven by tet methylcytosine dioxygenase 2 (Tet2) mutations and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which was associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and replication protein A complex. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies.

Authors

Zuzana Tothova, Anne-Laure Valton, Rebecca A. Gorelov, Mounica Vallurupalli, John M. Krill-Burger, Amie Holmes, Catherine C. Landers, J. Erika Haydu, Edyta Malolepsza, Christina Hartigan, Melanie Donahue, Katerina D. Popova, Sebastian Koochaki, Sergey V. Venev, Jeanne Rivera, Edwin Chen, Kasper Lage, Monica Schenone, Alan D. D’Andrea, Steven A. Carr, Elizabeth A. Morgan, Job Dekker, Benjamin L. Ebert

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Figure 5

STAG2 loss disrupts normal chromatin folding and association with DNA replication and damage repair proteins.

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STAG2 loss disrupts normal chromatin folding and association with DNA re...
(A) Hi-C interaction maps for chromosome 1 binned at 100 kb in WT vs. STAG2-knockout cells to visualize compartments. Arrowheads depict examples of weakened compartments. (B) Saddle plots of Hi-C data binned at 100 kb resolution normalized by genomic distance. The saddle plot demonstrates global weakening of compartments in STAG2-knockout cells. Heatmaps were generated using Hi-glass from pooled reads from 2 independent WT (U937 WT-1, WT-2) and STAG2-knockout (U937 STAG2-KO3, STAG2-KO4) cell lines. EV1, first eigenvector. (C) Hi-C interaction maps for a genomic region in chromosome 5 binned at 25 kb in WT vs. STAG2-knockout cells to visualize TADs. Heatmaps were generated using Hi-glass from pooled reads from 2 independent WT (U937 WT-1, WT-2) and STAG2-knockout (U937 STAG2-KO3, STAG2-KO4) cell lines. Arrowheads depict examples of loss of TAD insulation. (D) Insulation score (42) as a function of distance from TAD boundaries demonstrates global weakening of insulation at TAD boundaries. (E) Hi-C interaction maps for a genomic region in chromosome 5 binned at 10 kb in WT vs. STAG2-knockout cells to visualize loops. Arrowheads depict examples of gain of longer loops. (F) Relationship between interaction frequency (P) and genomic distance (s) to estimate the average loop size and density demonstrates longer extruded loops in STAG2-knockout cells compared with WT cells (represented by dashed lines, U937 WT1, WT2 ~100 kb; U937 STAG2-KO3, KO4 ~200 kb) and the density of loops is reduced in STAG2-knockout cells (represented by dotted lines). (G) Structured illumination microscopy of SMC1A and PARP1 in WT (U937 WT-1, WT-2) and STAG2-knockout (U937 STAG2-KO-3, STAG2-KO5) cells. Fluorescence signal displayed alone and merged with the nuclear Hoechst stain. Quantification of colocalization of SMC1A with PARP1 or RPA1 was determined using Manders colocalization coefficient. Original magnification, 100×. Box and whiskers represent mean ± Tukey’s. *P < 0.0001, unpaired Student’s t test.