Fei Li^1,2,9, Yizhe Wang^3,9, Inah Hwang^3,4,9, Ja-Young Jang³, Libo Xu^2,5, Zhong Deng⁶, Eun Young Yu⁷, Yiming Cai⁸, Caizhi Wu², Zhenbo Han⁸, Yu-Han Huang², Xiangao Huang³, Ling Zhang^2,5, Jun Yao⁸, Neal F. Lue⁷, Paul M. Lieberman⁶, Haoqiang Ying⁸, Jihye Paik³ & Hongwu Zheng³

¹Department of Neurosurgery, Southwest Hospital, Chongqing 400038, China. 
²Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. 
³Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA. 
⁴Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea. 
⁵Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China. 
⁶The Wistar Institute, Philadelphia, PA 19104, USA. 
⁷Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY 10065, USA. 
⁸Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA. 
⁹These authors contributed equally: Fei Li, Yizhe Wang, Inah Hwang.

Corresponding authors : Correspondence to Jihye Paik or Hongwu Zheng.

Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% − 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following recombination-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.