ATM-dependent DNA damage response constrains cell growth and drives clonal hematopoiesis in telomere biology disorders
Christopher M. Sande, et al.
Christopher M. Sande, et al.
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Research Article Hematology Oncology

ATM-dependent DNA damage response constrains cell growth and drives clonal hematopoiesis in telomere biology disorders

Abstract

Telomere biology disorders (TBDs) are genetic diseases caused by defective telomere maintenance. TBD patients often develop bone marrow failure and have an increased risk of myeloid neoplasms. To better understand the factors underlying hematopoietic outcomes in TBD, we comprehensively evaluated acquired genetic alterations in hematopoietic cells from 166 pediatric and adult TBD patients. Of these patients, 47.6% (28.8% of children, 56.1% of adults) had clonal hematopoiesis. Recurrent somatic alterations involved telomere maintenance genes (7.6%), spliceosome genes (10.4%, mainly U2AF1 p.S34), and chromosomal alterations (20.2%), including 1q gain (5.9%). Somatic variants affecting the DNA damage response (DDR) were identified in 21.5% of patients, including 20 presumed loss-of-function variants in ataxia-telangiectasia mutated (ATM). Using multimodal approaches, including single-cell sequencing, assays of ATM activation, telomere dysfunction-induced foci analysis, and cell-growth assays, we demonstrate telomere dysfunction–induced activation of the ATM-dependent DDR pathway with increased senescence and apoptosis in TBD patient cells. Pharmacologic ATM inhibition, modeling the effects of somatic ATM variants, selectively improved TBD cell fitness by allowing cells to bypass DDR-mediated senescence without detectably inducing chromosomal instability. Our results indicate that ATM-dependent DDR induced by telomere dysfunction is a key contributor to TBD pathogenesis and suggest dampening hyperactive ATM-dependent DDR as a potential therapeutic intervention.

Authors

Christopher M. Sande, Stone Chen, Dana V. Mitchell, Ping Lin, Diana M. Abraham, Jessie Minxuan Cheng, Talia Gebhard, Rujul J. Deolikar, Colby Freeman, Mary Zhou, Sushant Kumar, Michael Bowman, Robert L. Bowman, Shannon Zheng, Bolormaa Munkhbileg, Qijun Chen, Natasha L. Stanley, Kathy Guo, Ajibike Lapite, Ryan Hausler, Deanne M. Taylor, James Corines, Jennifer J.D. Morrissette, David B. Lieberman, Guang Yang, Olga Shestova, Saar Gill, Jiayin Zheng, Kelcy Smith-Simmer, Lauren G. Banaszak, Kyle N. Shoger, Erica F. Reinig, Madilynn Peterson, Peter Nicholas, Amanda J. Walne, Inderjeet Dokal, Justin P. Rosenheck, Karolyn A. Oetjen, Daniel C. Link, Andrew E. Gelman, Christopher R. Reilly, Ritika Dutta, R. Coleman Lindsley, Karyn J. Brundige, Suneet Agarwal, Alison A. Bertuch, Jane E. Churpek, Laneshia K. Tague, F. Brad Johnson, Timothy S. Olson, Daria V. Babushok

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Figure 7

Single-cell transcriptome analysis of hematopoietic cells in TBD patients compared with healthy controls.

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Single-cell transcriptome analysis of hematopoietic cells in TBD patient...
(A) UMAP plot of bone marrow mononuclear cells (BMMCs) from 2 healthy controls and 2 patients with TBD. (B) UMAP plot of peripheral blood mononuclear cells (PBMCs) from 4 healthy controls and 1 patient with TBD. (C) A lollipop plot of gene set enrichment analysis (GSEA) of single-cell transcriptomes in BMMCs from 2 patients with TBD compared with 2 healthy controls (left side of the panel) and in PBMCs from 1 patient with TBD compared with 4 healthy controls (right side of panel). Shown are the results demonstrating significantly dysregulated pathways (listed on the y axis) across analyzed cell clusters (shown on the x axis in BMMCs: early myeloid, hematopoietic stem cells [HPSCs], early erythroid, T cells, and in PBMCs: Monocytes, T cells). Adjusted P value is indicated by a color scale, from yellow (P = 0.000) to teal (P = 0.050) to blue (P = 0.1), with gray representing adjusted P value >0.1. The absolute enrichment score is indicated by the size of the circle, and normalized enrichment score is indicated by the direction and length of the lollipop stem. ATM-dependent DDR, Fas, and mitotic spindle pathways were upregulated across subsets, with the corresponding downregulation of pathways in S phase, DNA replication, Myc targets, and translation. (D and E) Histograms showing significant differences with a reduction in S phase and increase in G2_M and G1 phases of the cell cycle in TBD patients compared with controls in BMMCs (D) and PBMCs (E). ***P < 0.001. (F) UMAP plot of BMMCs showing expression of ATM in patients versus controls.