Abstract B045: Targeted degradation of cyclin T1 constrains transcription elongation and triggers tumour cell apoptosis

Abstract PR010: Targeted degradation of cyclin T1 constrains transcription elongation and triggers tumour cell apoptosis

Transcriptional dysregulation is a hallmark of cancer and is frequently driven by oncogenic alterations that rewire downstream gene-expression programmes. Although kinase inhibitors targeting upstream oncogenic drivers can produce clinical benefit, responses are often limited by acquired resistance and pathway adaptation. Targeting transcriptional dependencies therefore represents an alternative therapeutic strategy. The positive transcription elongation factor b complex, composed of CDK9 and Cyclin T1(CCNT1), is a central regulator of RNA polymerase II transcriptional elongation and supports the expression of genes required for tumour cell survival. However, conventional CDK9 inhibitors often lack sufficient selectivity and are associated with dose-limiting toxicities. Here, we report the rational design of a novel CCNT1-targeting binder and its application in biological proteolysis-targeting chimeras designed to selectively degrade Cyclin T1. The degrader platform combines E3 ubiquitin ligase recruitment with a dual-peptide CCNT1-binding module derived from the pTEFb-interacting partners AFF4 and HIV-TAT. This engineered recruitment strategy enabled robust and selective depletion of both tagged and endogenous CCNT1 in cancer cells. CCNT1 degradation was accompanied by destabilisation of its catalytic partner CDK9 and reduced phosphorylation of RNA polymerase II, consistent with suppression of transcriptional elongation. Functionally, CCNT1-targeted degradation produced marked anti-tumour effects in lung cancer models. Degrader-treated cells showed impaired proliferative capacity, reduced colony formation, cell-cycle disruption across multiple checkpoints, and induction of apoptosis. These findings demonstrate that selective degradation of CCNT1 can effectively collapse pTEFb-dependent transcriptional programmes and compromise tumour cell fitness. Together, our study establishes a novel CCNT1 binder-enabled degrader strategy as a translational approach to targeting transcriptional addiction in cancer. By moving beyond catalytic CDK9 inhibition and directly eliminating the Cyclin T1 scaffold, CCNT1-targeted degradation may offer a more selective and durable route for therapeutic intervention in transcriptionally dependent tumours. Janice Wenzheng Neng, Laura Blenkarn, Laura S. Itzhaki, Catherine H. Wilson. Targeted degradation of cyclin T1 constrains transcription elongation and triggers tumour cell apoptosis [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr PR010.

Nuclear-targeted GDOWN1 potently suppresses tumors by inducing premature transcription termination and exporting Pol Ⅱ CTD phosphatases to activate RB.

BAF perturbation heightens cancer cell dependence on CDK12-driven transcription elongation by RNA polymerase II

CDK12 facilitates transcriptional elongation and processivity by RNA polymerase II (Pol II). Although it has emerged as a promising actor and target in cancer, better understanding of CDK12 gene transcription control could inform the design of novel anti-cancer strategies. Here, we identify a co-dependency between CDK12 and the BAF chromatin-remodeling complex in triple-negative breast cancer (TNBC). Genome-scale CRISPR interference screening revealed multiple BAF subunits as strong dependencies upon CDK12 inhibition. In turn, pharmacological co-targeting of CDK12 and BAF ATPase synergistically reduced the viability of multiple TNBC models. Mechanistically, the co-inhibition attenuated di-phosphorylation of the Pol II C-terminal domain at Serine-2 and Serine-5 and depleted canonical pre-mRNA 3′-end processing factors from chromatin, driving accumulation of chromatin-associated Pol II, upstream of apoptosis. Whereas BAF inhibition rapidly reduced transcription-coupled DNA accessibility, CDK12 inhibition imposed a gene length-biased transcriptional defect exacerbated by BAF deficiency. In turn, co-inhibited cells, marked by synergistic induction of MYC and repression of long cell-cycle and mitotic genes, showed a failure of DNA synthesis and mitotic entry, culminating in MYC-mediated apoptosis. Together, our findings reveal a regulatory axis in which impaired Pol II elongation creates a heightened requirement for BAF-dependent chromatin remodeling. This discovered co-dependency provides a rationale for co-targeting the CDK12-BAF axis in transcriptionally addicted cancers.

Targeted degradation of P-TEFb via MDM2 substrate substitution collapses oncogenic transcriptional programs in MDM2-amplified cancers

MDM2 is an oncogenic E3 ubiquitin ligase best known for targeting the tumor suppressor p53 and is frequently amplified in human cancers, including dedifferentiated liposarcoma (DDLPS). We show that supraphysiological MDM2 expression can be exploited to reprogram its ligase activity toward selective degradation of oncogenic transcriptional machinery. Using a substrate substitution strategy, we developed an MDM2-recruiting degrader dCDK9-010 that targets positive transcription elongation factor b, inducing its proteasomal degradation while simultaneously stabilizing p53. This dual action disrupts RNA polymerase II abundance and elongation, preferentially impairing enhancer-driven transcriptional programs that sustain tumor growth. In DDLPS models, this approach produces potent antitumor activity with favorable pharmacokinetic and safety profiles, triggers apoptosis, and enhances macrophage-mediated tumor cell clearance. These findings establish substrate substitution-based reprogramming of MDM2 as a generalizable targeted protein degradation strategy and identify MDM2 amplification as a predictive biomarker for therapeutic response across cancer types, with particular relevance to liposarcoma.

Molecular targeting of CDK9 in oncology therapeutics: avenues for translational impact.

BACKGROUND Cyclin-dependent kinase 9 (CDK9) is a central regulator of RNA polymerase II elongation and has emerged as a therapeutic target in tumors characterized by transcriptional addiction. Growing interest in selective inhibitors and targeted degraders has renewed attention to the translational potential of CDK9-directed therapy. AREAS COVERED This review summarizes the molecular functions of the CDK9/positive transcription elongation factor b (P-TEFb) axis, its role in super-enhancer-driven oncogenic programs, and the mechanisms by which CDK9 inhibition promotes apoptosis, epigenetic derepression, and tumor microenvironment remodeling. We also discuss representative small-molecule inhibitors and proteolysis-targeting chimera (PROTAC) degraders, emerging biomarkers for patient stratification, rational combination strategies, and the current landscape of resistance mechanisms. EXPERT OPINION Selective targeting of CDK9 offers a promising route for treating refractory malignancies, particularly when guided by transcriptional dependency, biomarker-informed dosing, and rational combination design. Future progress will likely depend on improving therapeutic index, refining translational biomarkers, and anticipating adaptive resistance during clinical development.

Abstract A053: Discovery and modular design of CDK12–DDB1 molecular glues for targeted Cyclin K degradation

Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) regulate transcriptional elongation, RNA processing, and DNA damage response programs essential for genome stability. Genetic alterations of CDK12 are recurrent across multiple tumor types, establishing this kinase as a compelling therapeutic target. While several ATP-competitive CDK12/13 inhibitors have been reported, recent evidence suggests that selected inhibitors can also function through induced-proximity mechanisms that promote selective protein degradation. SR-4835, originally discovered and reported by our group as a potent and selective ATP-competitive CDK12/13 inhibitor in 2019, has since become a widely used, commercially available tool compound to interrogate CDK12/13 biology in vitro and in vivo. Subsequent mechanistic studies revealed that SR-4835 acts as a molecular glue, promoting formation of a ternary complex between CDK12-cyclin K and the DDB1-CUL4-RBX1 E3 ubiquitin ligase, resulting in proteasome-mediated degradation of cyclin K. Notably, the extent of cyclin K degradation correlates with ternary complex formation rather than catalytic inhibition of CDK12. Building on this foundation, we applied structure-guided optimizations to demonstrate that molecular glue activity is not restricted to a single scaffold. Introduction of solvent-exposed benzimidazole substituents capable of engaging DDB1 enabled conversion of multiple CDK12-directed inhibitor scaffolds into effective cyclin K degraders, establishing structure-degradation relationships that are separable from classical kinase SAR. Proteome-wide profiling confirmed cyclin K as a consistently degraded target across optimized compounds. In vitro target engagement was confirmed using CRISPR/HiBiT-tagged reporter cell lines and quantitative immunofluorescence imaging, demonstrating compound-induced cyclin K degradation. In HER2+ and TNBC xenograft models, these compounds elicited rapid, dose-dependent cyclin K loss and robust antitumor efficacy, establishing tumor cyclin K degradation as a quantitative PD biomarker and demonstrating in vivo proof of mechanism in PDX cancer models. Advanced lead molecules across these series achieve a rare combination of high CDK12/13 selectivity, potent and durable cyclin K degradation, and favorable physicochemical, in vitro ADME, and in vivo PK properties, supporting progression toward IND-enabling preclinical safety evaluation. Thiyagamurthy Pandurangan, Anna Iermolaieva, Pompom Ghosh, John Mosior, Luxin Sun, Dylan Grassie, Matthias Geyer, Ernst Schönbrunn, William Roush, Derek Duckett, Andrii Monastyrskyi. Discovery and modular design of CDK12–DDB1 molecular glues for targeted Cyclin K degradation [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr A053.