Abstract Phosphoinositides (PIs) are a class of lipid second messengers that coordinate signaling events at the membrane interface. This canonical role belies the presence of rich PI metabolism within the nucleus, where emerging functions reveal pivotal contributions to oncogenesis. Despite this, effectors that transduce this lipid network are largely obscure. In particular, dysregulation of nuclear phosphatidylinositol 4,5-bisphosphate (PI4,5P2) and its generative kinases PIPKIIα and PIPKIIβ are salient in breast cancer progression and prognosis, yet the mechanistic basis for how they drive oncogenesis remains enigmatic. Identification of the underlying pathways, therefore, remains a critical question that could inform novel therapeutic strategies. To investigate their nuclear function, we examined PI4,5P2 dynamics by immunofluorescence (IF) and observed accumulation at γH2A.X-positive DNA lesions. Consistent with this, DNA damage response (DDR) assays quantifying caspase activation, growth and genomic integrity revealed that PIPKIIα/β double-knockout breast cancer cells exhibited genotoxic hypersensitivity and exacerbated genomic fragmentation. These observations implicated PIPKIIα/β in DDR signaling. Through mass spectrometric profiling of nuclear extracts, we identified CK2α as an interactor of PIPKIIα and PIPKIIβ. This interaction was validated by endogenous co-immunoprecipitation and further supported by in vitro binding assays between purified recombinant proteins and proximity ligation immunofluorescence, which together revealed direct and nuclear-restricted engagement. Cells lacking PIPKIIα/β selectively compromised CK2α activity elicited in response to DNA damage, but not mitogenic stimulation. Interrogation of CK2α-dependent DDR substrates further demonstrated impaired downstream signaling, substantiating PIPKIIα/β control over CK2α in the DDR. To probe lipid signaling transduction, we performed structural, biochemical, and in silico assays that uncovered a PI-binding polybasic motif (PBM) in CK2α (residues 71-80) adjacent to the binding interface of its regulatory subunit CK2β; further mutation of this PBM diminished PI4,5P2 binding. This motivated the hypothesis that PI4,5P2 supplants CK2β, releasing monomeric CK2α, thereby redirecting its substrate specificity. Accordingly, PIPKIIα/β depletion enhanced endogenous CK2α-CK2β association while concurrently diminishing its interaction with the DDR-substrate XRCC1. Our findings support a model in which PIPKIIα/PIPKIIβ synthesizes PI4,5P2 following DNA damage to liberate nuclear CK2α from CK2β and potentiate the DDR. Late-stage breast cancers may upregulate this pathway to mitigate otherwise lethal genetic insults and promote survival against their intrinsic genomic instability, defining a previously unrecognized nuclear PI4,5P2 signaling axis that promotes tumor progression. Citation Format: Gavril Limet Ibaan, Suyong Choi. CK2α is a novel phosphoinositide effector of PIPKIIα and PIPKIIβ in DNA damage repair abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4699.
Ibaan et al. (Fri,) studied this question.