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 3

Development of primary models of cohesin-mutant MDS.

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Development of primary models of cohesin-mutant MDS. (A) Schematic of th...
(A) Schematic of the sequential bone marrow transplant used to generate Tet2/Stag2-mutant models of myeloid disease. (B) Morphologic evaluation of bone marrow section of mice injected with NTG and Tet2-mutant cells. H&E staining, 10× magnification. No appreciable differences were observed. Scale bar: 0.5 mm. (C) Flow cytometry analysis of peripheral blood (PB) samples of mice sequentially transplanted with Tet2/NTG and Tet2/Stag2 3 months after transplantation. Blue fluorescent protein (BFP) reporter is linked to expression of sgRNA targeting Stag2, and red fluorescent protein (RFP) reporter is linked to expression of sgRNA targeting Tet2. Expansion of BFP+ and BFP+RFP+ cells in Tet2/Stag2 animals. n = 7 per arm. Mean ± SD shown. (D) Absolute white blood cell (WBC) count, neutrophil count, lymphocyte count, monocyte count, hematocrit, and platelet count were measured in Tet2/NTG and Tet2/Stag2-mutant mice 12 weeks after bone marrow transplantation. Mean ± SD is shown. P values were determined using the Student’s t test. n = 20 mice per group. (E) Morphologic evaluation of bone marrow of a representative Tet2/NTG and Tet2/Stag2-mutant mouse shows a decrease in megakaryocytes and increased erythrophagocytosis in Tet2/Stag2-mutant mice. Images were stained using H&E and imaged at 10× (scale bar: 0.5 mm) and 40× (scale bar: 0.125 mm) original magnification.