Biology subjects

McGrail, J. C.

Publications and source records attributed to McGrail, J. C..

3 recordsLinked to original sources

bioRxiv2025

Transcriptional Circuitry in HGSOC: A Dynamic Three-State Model Informed by a Living Biobank of Purified Tumour Fractions

High-grade serous ovarian cancer (HGSOC) is a heterogeneous disease, but efforts to define transcriptional subtypes using bulk RNA sequencing have been confounded by the presence of non-malignant cells. As a result, it remains unclear whether tumour-cell-intrinsic states exist, and whether these represent stable disease subtypes or are dynamically remodelled during disease progression and treatment. Here, we address this question using a living biobank of patient-derived ovarian cancer models (OCMs) cultured as purified tumour-cell populations under uniform conditions. RNA sequencing followed by unsupervised non-negative matrix factorisation (NMF) revealed a robust, hierarchical architecture comprising three core tumour-cell-intrinsic subtypes: the Alpha cluster, marked by cell-cycle deregulation and E2F-driven replication stress; the Beta cluster, defined by tumour-cell-intrinsic immune mimicry and inflammatory signalling; and the Gamma cluster, characterised by epithelial identity, extracellular matrix engagement, and metabolic adaptation. At higher clustering resolution, a fourth cluster, Delta, emerged as a Gamma sub-lineage distinguished by a vesicle-oriented, neuronal-like secretory programme. By projecting cluster labels onto a subset of matched longitudinal OCMs using non-negative least squares, we show that while some tumours retain stable subtype identities, others display transcriptional plasticity, including transitions from epithelial-like Gamma states to more proliferative or secretory phenotypes. Together, these findings define the core architecture and dynamic potential of tumour-cell-intrinsic transcriptional states within HGSOC, thereby bridging legacy bulk classifications with emerging single-cell insights, establishing a framework for more precise patient stratification.

cancer biology↗

bioRxiv2025

Exploring CDK4/6-Dependencies in ex vivo Ovarian Cancer Models

Ovarian cancer (OC) is a clinically and molecularly heterogeneous disease with limited treatment options for the majority of patients, particularly those with homologous-recombination-proficient high-grade serous ovarian cancer (HGSOC) and rarer subtypes such as low-grade serous ovarian cancer. Deregulation of the G1/S cell cycle network is common across all subtypes, suggesting subtype-agnostic vulnerabilities. Here, we assessed CDK4/6 dependency using the selective inhibitor palbociclib across 20 patient-derived ex vivo OC models. A subset of models, including four HGSOC and six rarer subtypes, exhibited marked sensitivity to palbociclib, characterised by low CDKN2A/CDKN2B expression, Rb hypophosphorylation, and G1 cell cycle arrest. In contrast, resistant models showed high CDKN2A expression and reduced or absent RB1. Notably, ABCB1 overexpression--a known resistance mechanism in OC--did not mediate palbociclib resistance. Analysis of longitudinal models revealed diminished CDK4/6 dependency following treatment, accompanied by increased CDKN2A expression. These findings support a model of G1/S control in which tumours diverge into CDK4/6- or CDK2-driven proliferation states, with CDKN2A as a potential biomarker to guide patient selection. The predominance of CDK4/6-inhibitor-resistant HGSOC highlights a priority population for CDK2-targeted therapies, offering new treatment strategies for patients with otherwise limited options.

cancer biology↗

bioRxiv2021

TP53 loss initiates chromosomal instability in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) originates in the fallopian tube epithelium and is characterized by ubiquitous TP53 mutation and extensive chromosomal instability (CIN). While the direct causes of CIN are errors during DNA replication and/or chromosome segregation, mutations in genes encoding DNA replication and mitotic factors are rare in HGSOC. Thus, the drivers of CIN remain undefined. We therefore asked whether the oncogenic lesions that are frequently observed in HGSOC are capable of driving CIN via indirect mechanisms. To address this question, we genetically manipulated non-transformed hTERT-immortalized human fallopian tube epithelial cells to model homologous recombination deficiency (HRD) and oncogenic signalling in HGSOC. Using CRISPR/Cas9-mediated gene editing, we sequentially mutagenized the tumour suppressors TP53 and BRCA1, followed by overexpression of the MYC oncogene. Single-cell shallow-depth whole-genome sequencing revealed that loss of p53 function was sufficient to lead to the emergence of heterogenous karyotypes harbouring whole chromosome and chromosome arm aneuploidies, a phenomenon exacerbated by subsequent loss of BRCA1 function. In addition, whole-genome doubling events were observed in independent p53/BRCA1-deficient subclones. Global transcriptomics showed that TP53 mutation was also sufficient to deregulate gene expression modules involved in cell cycle commitment, DNA replication, G2/M checkpoint control and mitotic spindle function, suggesting that p53-deficiency induces cell cycle distortions that could precipitate CIN. Again, loss of BRCA1 function and MYC overexpression exacerbated these patterns of transcriptional deregulation. Thus, our observations support a model whereby the initial loss of the key tumour suppressor TP53 is sufficient to deregulate gene expression networks governing multiple cell cycle controls, and that this in turn is sufficient to drive CIN in pre-malignant fallopian tube epithelial cells. SUMMARY STATEMENTHigh-grade serous ovarian cancer is defined by TP53 mutation and chromosomal instability, the cause of which remains poorly understood. We developed a novel model system that implicates cell cycle deregulation upon p53-loss as cause of CIN.

cancer biology↗