Anthony J. Davis

Background: Solid tumors including glioblastoma (GBM), lung cancer (LC), and triple-negative breast cancer (TNBC) exhibit marked radioresistance driven by dysregulated cell-cycle control and genomic instability. Although CDK4/6 inhibitors suppress tumor proliferation, their radiosensitizing capacity is limited by persistent DNA repair. BUB1, a mitotic checkpoint kinase overexpressed in aggressive cancers, has emerged as a regulator of DNA damage signaling. We tested whether co-targeting BUB1 and CDK4/6 enhances radiosensitivity across solid tumors. Methods: GBM, LC, and TNBC cell lines were treated with BUB1 inhibitor BAY1816032, CDK4/6 inhibitors ribociclib and abemaciclib, and radiation. Proliferation, clonogenic survival, immunoblotting, and combination index analyses assessed cytotoxicity and synergy. CDK4/6-resistant models were generated to examine resistance. In vivo efficacy was evaluated using SUM159 xenografts. DNA damage and homologous recombination repair were measured by gH2AX, RAD51, RPA, BrdU foci and comet assay. The resection branchpoint was assessed by phospho-RPA, with ATR inhibition and BLM or EXO1 depletion testing resection dependence. Results: BUB1 inhibition increased cytotoxicity in vitro and improved therapeutic response in vivo. Combined BUB1 and CDK4/6 inhibition showed strong synergy (C.I. < 1) and enhanced radiosensitization in RB+ models. CDK4/6-resistant cells displayed increased BUB1 expression, and BUB1 inhibition partially restored sensitivity. Mechanistically, dual inhibition intensified homologous recombination defects, marked by persistent gH2AX and altered RAD51, RPA, and BrdU dynamics, consistent with sustained single stranded DNA and impaired HR repair. Persistent RPA32 Ser33 phosphorylation reflects ATR-dependent resection that requires BLM and EXO1 at later stages, supporting sustained resection and unresolved repair leading to increased cell death. Conclusions: Dual inhibition of BUB1 and CDK4/6 represents a promising therapeutic strategy for enhancing radiosensitivity in GBM, lung cancer, and TNBC, particularly in Rb-intact settings.

DNA mismatch repair (MMR) deficiency has been widely utilized in forward genetic screens to identify drug resistance mutations and elucidate the mechanisms of action of cytotoxic small molecules. However, MMR deficiency generates a characteristic mutational signature enriched for C>T transitions that precludes saturation of mutagenesis. We hypothesized that expression of proofreading deficient DNA polymerase epsilon, as has been observed in patients with biallelic MMR deficiency, would enhance mutagenesis and enable identification of new resistance mutations and cytotoxin mechanisms. Here, we combine auxin-inducible degradation of Msh2 with doxycycline-inducible expression of the proofreading-deficient Polε ^P286R mutant in murine small cell lung cancer (SCLC) cells. Simultaneous MMR deficiency and mutant Polε expression markedly increased the emergence of bortezomib-resistant clones relative to either perturbation alone and targeted sequencing of Psmb5 in bortezomib-resistant clones identified recurrent mutations previously reported in chemical mutagenesis-based resistance screens. We next applied this platform to investigate resistance to lurbinectedin, a clinically relevant therapy for SCLC. Whole-exome sequencing revealed recurrent loss-of-function alterations in nucleotide excision repair (NER) genes, most notably Ercc5 and Ercc4 , implicating NER deficiency as a major mechanism of lurbinectedin resistance and supporting a central role for NER in mediating lurbinectedin-induced cytotoxicity. Collectively, these findings establish inducible ultramutagenesis as a powerful and versatile platform for the unbiased discovery of drug resistance mechanisms and therapeutic vulnerabilities.

Replication stress (RS) and altered metabolism are two hallmarks of cancer, yet how metabolic perturbations contribute to RS remains poorly understood. Lipotransferase 1 (LIPT1) catalyzes the covalent attachment of lipoic acid to mitochondrial 2–ketoacid dehydrogenases, sustaining flux through the tricarboxylic acid (TCA) cycle. Loss of LIPT1 causes accumulation of 2-hydroxyglutarate (2-HG), which is known to inhibit α-ketoglutarate (α-KG)–dependent histone demethylases and promotes heterochromatin formation. Here, we show that 2-HG–driven heterochromatin impedes replication fork progression, causing fork stalling and RS in LIPT1-deficient cancer cells. To bypass stalled forks, PrimPol-mediated repriming resumes DNA synthesis but leaves behind single-stranded DNA (ssDNA), which requires poly(adenosine 5′-diphosphate–ribose) polymerase 1 (PARP1) for repair. Furthermore, nascent DNA at reprimed forks undergoes MRE11-dependent degradation, further destabilizing replication fork integrity. Consequently, LIPT1 deficiency promotes replication and genome instability, and therapeutic vulnerability to PARP inhibitor. Together, these findings reveal a mechanistic link between mitochondrial lipoylation and replication fork stability, uncovering a metabolic basis for genome instability in cancer.

Supplementary Figure 2 shows scRNAseq therapy experiment phenotyping, response and resistance modules, and expression of targetable genes.

Raw data tables for sequencing data from figures 2 and 5.

Supplementary Figure 1 shows survival, tumor growth and radiation response of various KPC tumor cell clones.

Supplementary Figure 3 shows cGas sting expression of various KPC clones and then carbon and photon treated KPC 36 implanted mouse response and survival.

The tumor landscape of pancreatic ductal adenocarcinoma (PDAC) is refractory to conventional photon radiotherapy (RT) because of a fibrotic tumor microenvironment (TME) that promotes chronic hypoxia and reduced immune surveillance. The radiobiological factors unique to carbon ion RT (CIRT), such as high linear energy transfer and less dependence on oxygen, make it well-suited to overcome the PDAC TME. In this study, we utilized clonal syngeneic KPC pancreatic tumor cell lines and tumors to examine this postulate and to identify underlying factors that affect the response of PDAC to CIRT. Although KPC cell lines exhibited radiobiological effectiveness greater than 3, subcutaneous tumors in the mouse hind leg showed lower radiobiological effectiveness—1.3 based on quintupling time—at a linear energy transfer between 70 and 80 keV/μm. Four days after CIRT, we observed widespread transcriptomic changes in the tumor immune microenvironment, suggesting increased infiltration of antitumor immune cells and elevated expression of antitumor T-cell cytokines, MHC class I molecules, and co-stimulatory signals. Fewer immunologic changes were observed following photon irradiation. By 7 days after CIRT, tumor-supportive transcriptomic programs characterized by protumor cytokines, M2 macrophages, and cancer-associated fibroblasts emerged, promoting resistance and limiting the durability of tumor growth delay. These findings suggest that CIRT may offer a favorable platform compared with conventional photon RT for combining with immunotherapies. Furthermore, these data highlight the risk of using in vitro survival data alone in treatment planning and indicate that underlying TME factors affect the response of PDAC in vivo.

Table of genes categories and genes defining the category for Figure 2F.

DAB2IP (Disabled homolog 2 interacting protein), a recognized tumor suppressor, plays a pivotal role in regulating various oncogenic pathways. Our previous research demonstrated that DAB2IP functions as a cell cycle regulator by facilitating PLK1-mediated mitosis progression. Here, we elucidate a novel function of DAB2IP in promoting DNA replication origin firing. Mechanistically, we identified that DAB2IP localizes to the nucleus, where it interacts with the histone acetyltransferase HBO1 and enhances the HBO1–PLK1 interaction. DAB2IP facilitates PLK1-mediated phosphorylation of HBO1, which subsequently promotes HBO1-directed acetylation of histone 3 at lysine 14 (H3K14Ac). This modification enables the loading of the minichromosome maintenance protein (MCM) complex onto chromatin, thereby supporting DNA replication and maintaining genome integrity. Additionally, we found that ATR regulates CDK1-mediated phosphorylation of DAB2IP, and that this phosphorylation is essential for the formation and activation of the HBO1-PLK1 complex. Ablation of DAB2IP phosphorylation results in increased genomic instability due to incomplete replication of genomic DNA, as evidenced by the accumulation of anaphase ultrafine bridges and 53BP1 nuclear bodies in G1 phase of the cell cycle. In summary, our findings underscore the critical regulatory role of DAB2IP in DNA replication initiation and genomic stability maintenance, providing new insights into its function in cellular homeostasis.