Biology subjects

Cloete, I.

Publications and source records attributed to Cloete, I..

5 recordsLinked to original sources

bioRxiv2025

Dynamical analysis of a model of BCL-2-dependent cellular decision making

The BCL-2 protein family governs critical cell-fate decisions between survival, senescence, and apoptosis, yet the dynamical principles underlying these choices remain poorly understood. Here, we integrate mathematical modeling, bifurcation analysis, and stochastic simulations to dissect how BCL-2 network architecture encodes multistability and fate plasticity. Our coarse-grained model reveals tristable regimes requiring cooperative BH3-only and anti-apoptotic BCL-2 interactions, with stochastic fluctuations driving heterogeneous fate commitments in genetically identical cells. Comparative analysis of mechanistic models demonstrates that while bistability emerges from canonical BCL-2 interactions, robust tristability requires additional regulatory constraint, explaining the metastability of senescence in stress responses. Hybrid models further show that BH3-only binding cooperativity enables multistability, but physiological senescence likely depends on additional control mechanisms. These results establish a unified framework linking molecular interactions to cell-fate dynamics, with implications for targeting apoptosis resistance in disease.

systems biology↗

bioRxiv2024

Targeted inhibition of Bcl-xL following radiation reduces tumourigenesis in preclinical models of H3K27M-altered diffuse midline glioma

BackgroundDiffuse midline gliomas (DMGs) with histone H3K27M mutations represent a devastating paediatric brain cancer characterized by abysmal prognosis and limited treatment options. The only approved treatment is radiotherapy (RT), but most of the tumours relapse with fatal consequences. In this study, we sought to investigate whether irradiation leads to senescence induction and explore the efficacy of senolytics against DMG. MethodsWe have characterised the senescent phenotype of five genetically heterogeneous H3K27M-altered human DMG cell lines, combining cellular and/or molecular approaches. The sensitivity of senescent cells to Bcl-xL inhibition has been demonstrated in dose/response curves in vitro and in a PDX model of DMG. ResultsHere, we show that ionizing radiation induces senescence and SASP responses in both TP53 mutant and wild-type H3K27M-altered human DMG cell lines. We identify Navitoclax as a potent senolytic agent that selectively targets senescent DMG cells into apoptosis by inhibiting Bcl-xL. Related compounds, such as a proteolysis-targeting chimera (PROTAC)-mediated Bcl-xL degradation and a galacto-conjugated form of Navitoclax also show an effective senolytic activity in senescent cancer cells. Finally, we show that a combination therapy of irradiation and Navitoclax results in reduced tumor burden and increased mouse survival in an orthotopic xenograft DMG model. ConclusionThese results offer a rationale for further clinical development of senolytic therapies as part of multimodal treatment approaches for DMG patients/ Key PointsO_LIIonising irradiation induces senescence in human DMG cells independently of the p53 status. C_LIO_LIBcl-xL inhibition results in apoptosis of human DMG senescent cells in synergy with irradiation. C_LIO_LICombination of irradiation and BcL-xL inhibition reduces tumourigenesis in a PDX model of DMG. C_LI Importance of the StudyH3K27M-altered DMG are devastating paediatric tumours with an abysmal prognosis. The only approved treatment is radiotherapy but this is palliative and tumours almost always relapse with fatal consequences for the patients. In this study, we show that radiotherapy results in senescence induction in five genomically heterogeneous human DMG cell lines. We identify that drugs targeting the anti-apoptotic protein Bcl-xL show a strong senolytic activity in conjunction with radiotherapy both in vitro in DMG cells and in vivo in a PDX model of H3K27M-altered DMG. Treatment with Bcl-xL inhibitor Navitoclax, or related compounds targeting Bcl-xL protein degradation or containing a galactose conjugated form of Navitoclax results in DMG cancer cell apoptosis. As several of these inhibitors are currently being tested in ongoing clinical trials against other diseases, our data support the use of Bcl-xL inhibition mediated senolytics as an adjuvant therapy to radiotherapy to potentially improve outcomes in this challenging disease setting.

cancer biology↗

bioRxiv2024

Pyruvate from bone marrow mesenchymal stem cells supports myeloma redox homeostasis and anabolism

Multiple myeloma is an incurable cancer of plasma cells that depends on the bone marrow for its survival. Despite its prevalence, the molecular mechanisms underlying this malignancy remain poorly understood. In this study, we aim to bridge this knowledge gap by elucidating the metabolic interplay between myeloma cells and bone marrow mesenchymal stem cells (BMMSCs). BMMSCs are crucial in supporting myeloma cell metabolism, contributing to their proliferation, survival, and resistance to chemotherapy. Through a combination of mathematical modelling and experimental co-cultures, we demonstrate that pyruvate - the end product of glycolysis - plays a key role in myeloma cell metabolism. Our findings reveal that myeloma cells predominantly rely on the uptake of pyruvate produced by neighbouring BMM-SCs via the plasma membrane proton-linked monocarboxylate transporters MCT-1 and MCT-2 encoded by the Slc16a1 and a2 genes, respectively. Furthermore, we show that pharmacological inhibition of the MCT-1/2, with AZD3965, triggers a cascade of compensatory metabolic responses, disrupting redox balance and significantly reducing the proliferation capacity of co-cultured myeloma cells.

cancer biology↗

bioRxiv2024

A Mathematical Exploration of SDH-b Loss in Chromaffin Cells

The succinate dehydrogenase (SDH) is a four-subunit enzyme complex (SDH-a, SDH-b, SDH-c, and SDH-d) central to cell carbon metabolism. The SDH bridges the tricarboxylic acid cycle to the electron transport chain. A pathological loss of the SDH-b subunit leads to a cell-wide signalling cascade that shifts the cells metabolism into a pseudo-hypoxic state akin to the so-called Warburg effect (or aerobic glycolysis). This trait is a hallmark of phaeochromocytomas, a rare tumour arising from chromaffin cells; a type of cell that lies in the medulla of the adrenal gland. In this study, we leverage the insights from a mathematical model constructed to underpin the metabolic implications of SDH-b dysfunction in phaeochromocytomas. We specifically investigate why chromaffin cells seemingly have the ability to maintain electron transport chains (ETC) Complex I function when confronted with the loss of the SDH-b subunit while other cells do not. Our simulations indicate that retention of Complex I is associated with cofactor oxidation, which enables cells to manage mitochondrial swelling and limit the reversal of the adenosine triphosphate (ATP) synthase, supporting cell fitness, without undergoing lysis. These results support previous hypotheses that point at mitochondrial proton leaks as a critical factor of future research. Moreover, the model asserts that control of the proton gradient across the mitochondrial inner membrane is rate-limiting upon fitness management of SDH-b deficient cells.

bioengineering↗

bioRxiv2023

Computational modeling of DLBCL predicts response to BH3-mimetics.

In healthy cells, pro- and anti-apoptotic BCL2 family and BH3-only proteins are expressed in a delicate equilibrium. In contrast, this homeostasis is frequently perturbed in cancer cells due to the overexpression of anti-apoptotic BCL2 family proteins. Variability in the expression and sequestration of these proteins in Diffuse Large B cell Lymphoma (DLBCL) likely contributes to variability in response to BH3-mimetics. Successful deployment of BH3-mimetics in DLBCL requires reliable predictions of which lymphoma cells will respond. Here we show that a computational systems biology approach enables accurate prediction of the sensitivity of DLBCL cells to BH3-mimetics. We found that fractional killing of DLBCL, can be explained by cell-to-cell variability in the molecular abundances of signaling proteins. Importantly, by combining protein interaction data with a knowledge of genetic lesions in DLBCL cells, our in silico models accurately predict in vitro response to BH3-mimetics. Furthermore, through virtual DLBCL cells we predict synergistic combinations of BH3-mimetics, which we then experimentally validated. These results show that computational systems biology models of apoptotic signaling, when constrained by experimental data, can facilitate the rational assignment of efficacious targeted inhibitors in B cell malignancies, paving the way for development of more personalized approaches to treatment.

systems biology↗