Biology subjects

Hooper, S.

Publications and source records attributed to Hooper, S..

10 recordsLinked to original sources

bioRxiv2025

Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma

Intra-tumour heterogeneity is a major obstacle to durable responses to targeted cancer therapy, yet how different resistant cell states interact within the same tumour remains poorly understood. In this study, we demonstrate cooperativity between co-occurring resistant states in a single tumour. Using BRAF mutant melanoma as a paradigm, we generate three different resistant states within a single model and demonstrate that they exhibit varying differentiation states and migratory capacities and share few common therapeutic vulnerabilities. Through a combination of experiments, including using Cre-mediated recombination to generate heterogeneity in existing tumours, and in silico modelling, we show that intra-tumour heterogeneity is the most favoured state for therapy resistant tumours. This is underpinned by signalling between different melanoma states, with YAP1 active cells providing supporting signals for other cells but inhibiting their own proliferation. Optimal disease control requires targeting both the YAP1 active cell state and the inter- cellular communication networks. We identify the histone demethylase inhibitor GSK-J4 as being particularly effective in targeting both features of resistant tumours and demonstrate its ability to control melanoma with multiple concurrent resistance mechanisms.

cancer biology↗

bioRxiv2025

Multicellular Calcium Waves in Cancer-Associated Fibroblasts Regulate Neuronal Mimicry and Anisotropy Leading to Immune Exclusion

Stromal barriers exclude CD8+ T cells from accessing cancer cells and hamper immune-mediated tumour control. Through multi-pronged analysis of tumours that transition from immune inflamed to immune excluded, we reveal that the formation of stromal barriers is associated with the acquisition of neuronal gene expression programmes in cancer-associated fibroblasts (CAFs), including TUBB3 expression. This leads to neuronal mimicry, with stromal barrier formation underpinned by coordinated transient bursts of intracellular calcium release, similar to those observed in neuronal tissue. Blockade of calcium release through either pharmacological or molecular interventions, such as STC2 depletion, prevents CAF alignment and the build-up of CD8+ T cells at stromal boundaries. Nintedanib treatment prevents neuronal mimicry and restores immune-mediated tumour control. Thus, we uncover unexpected mimicry of neuronal behaviour in CAFs, document the mechanism by which it leads to immune exclusion, and identify ways to prevent the induction of neuronal mimicry and restore immune-mediated tumour control. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/684281v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@938ee5org.highwire.dtl.DTLVardef@18a9c48org.highwire.dtl.DTLVardef@11a5982org.highwire.dtl.DTLVardef@ea6a79_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Rapid expansion of podoplanin-positive fibroblasts following radiation limits the anti-tumour CD8+ T-cell response to radiotherapy.

Radiotherapy is known to cause changes in the tumour stroma which can undermine treatment efficacy. Our understanding of this process has historically centred around effects driven by Transforming Growth Factor-beta (TGF-{beta}) and alpha-smooth muscle actin (-SMA)+ fibroblasts. Here, we identified a rapid expansion of podoplanin (PDPN)+ fibroblasts following radiotherapy in breast, head and neck and melanoma tumours. This fibrosis was not dependent on TGF-{beta}, but was downstream of a radiotherapy-induced adaptive immune response. CD8+ T-cells entering the tumour after radiation were sequestered at the interface between residual tumour cells and PDPN+ fibroblasts and failed to enter the tumour core. Genetic deletion of PDPN in fibroblasts impacted their cytoskeleton and ability to organise extracellular matrix. This was associated with increased CD8+ T-cell entry and spontaneous tumour regression. Overall, we identify a mechanism whereby PDPN+ fibrosis limits immune-mediated radiation cell kill and demonstrate that disruption of PDPN signalling favours tumour control. SignificanceIn this study we show that rapid podoplanin (PDPN)+ fibroblast expansion following radiotherapy limits immune-mediated radiation cell kill. Targeting PDPN and associated downstream signalling improves tumour control and is a promising strategy in combination with radiotherapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/680949v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1711bb0org.highwire.dtl.DTLVardef@d0c3a1org.highwire.dtl.DTLVardef@1db88adorg.highwire.dtl.DTLVardef@1ea3ab6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Splenic granulopoiesis and S100A9 drive resistance to checkpoint inhibitors conferred by liver metastases

Here, we investigate why liver metastases reduce the efficacy of immune checkpoint inhibitors (CPI). The poor prognosis of patients with liver metastases is associated with a systemic increase in neutrophils. Using experimental models, we confirm that mice with liver metastases respond poorly to CPI, have elevated neutrophils and suppress the response of subcutaneous lesions to CPI. We demonstrate that liver metastases, acting partly via IL-6, boost granulopoiesis in the spleen and promote the generation of immature S100A9hi neutrophils that suppress T-cell proliferation. Human liver metastases exhibit a similar increase in S100A9hi neutrophils. Neutrophil depletion attenuates the growth of liver metastases, but not subcutaneous metastases. Moreover, genetic deletion of S100A9 enables liver metastases to be effectively treated with CPI, and prevents liver metastases from suppressing the response in subcutaneous metastases. Thus, we document how liver metastases specifically change splenic granulopoiesis leading to changes in the microenvironment of non-hepatic lesions, and how targeting a key neutrophil protein restores the efficacy of CPI.

immunology↗

bioRxiv2025

Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer

The evolution of cancer undermines the long-term efficacy of therapy. In this study, we combine experimental, computational, and clinical data analysis to investigate factors influencing the competition of subclones in lung cancer. Lineage tracing reveals unexpected variation in the long-term fate of neutral subclones, with subclones arising near the edge of tumours being favoured. Low levels of cell migration and cell mixing lead to high cell densities in the interior of the tumour that suppress proliferation. Using agent-based modelling and in silico analysis we inferred the extent of cell mixing in human tumours from the TRACERx lung cancer study. This reveals correlations between Epithelial to Mesenchymal Transition (EMT), stromal fibroblasts and levels of cell mixing. Experimental analysis confirms that both TGF{beta}-driven EMT and stromal fibroblasts reduce the variability in subclone fate and promote subclone mixing. Moreover, mixing favours clonal sweeps by subclones resistant to therapy-induced cell killing. Together, these analyses demonstrate that EMT and stromal fibroblasts sculpt tumour evolution by promoting cell mixing and thereby favour the rapid dominance of therapy resistant subclones.

cancer biology↗

bioRxiv2024

Imaging of MAP kinase dynamics reveals endocytic regulation of pulsatile signalling and network re-wiring in response to targeted therapy in EGFR-mutant non-small cell lung cancer

A better understanding of the signalling mechanisms underlying transitions from drug-sensitive to drug-tolerant states is required to overcome therapy failure. We combined single-cell biosensor imaging with functional perturbations to investigate the regulation of oncogenic signalling in EGFR-mutant lung adenocarcinoma. We find that despite the constant presence of the mutant oncogene, ERK signalling exhibits pulsatile dynamics, with pulse characteristics determined by the endocytic machinery. Analysis of drug-tolerant persisters (DTPs) revealed that, after an initial phase of complete pathway shut-down, signalling was rewired leading to renewed ERK pulses that drive cell cycle progression. FAK- and SRC-regulated adhesion complexes replace mutant EGFR as the driver of reactivated ERK pulses in DTPs, yet they remain controlled by the membrane trafficking machinery. We show that DTPs rely on additional survival pathways including YAP signalling, and that the phosphatase PTPRS represents a key node in therapy resistant cells, coordinating regulation of ERK, the cytoskeleton, and YAP.

cancer biology↗

bioRxiv2024

An algorithm for identifying task-specific brain subnetworks using the visuomotor system as an example

We describe an algorithm that identifies a subnetwork of brain regions involved in producing a task-specific behavior, here visuomotor behavior, from an anatomically defined primate brain connectome. The algorithm first finds the brain regions connected to an output region (here, primary motor cortex, M1) by one connection. It then identifies all regions, termed "layer 2" regions, connected to these "layer 1" regions by one connection. This process continues until the layer containing the input region (here, primary visual cortex, V1) is reached. The algorithm then finds, subject to a user-set maximum step number, all paths linking the input and output regions. The brain regions in these paths constitute the initial subnetwork identification that performs the task. Regions known not to be task-involved (for example, regions in the ventral stream of visual information vs. the dorsal stream, which helps generate visuomotor behavior) are then removed. Structural subnetwork analysis showed that the intraparietal sulcus of the parietal cortex (PCIP) was most, and the secondary visual (V2) and superior parietal (PCS) cortices second-most, central to local network activity. Changing PCIP, V2 and PCS activity was thus most likely to alter activity of the entire subnetwork. Model sufficiency was tested by instantiating each brain regions inherent activity with multiple versions of a simple two-dimensional (2D) model that can produce oscillatory activity and synaptically interconnecting the regions to produce a macroscopic visuomotor model. The model reproduced the experimental local field potential (LFP) activity of the brain regions identified as part of the visuomotor subnetwork.

neuroscience↗

bioRxiv2023

Cancer cell - fibroblast crosstalk signature promotes macrophage recruitment via HB-EGF and stromal EGFR/MEK signalling

Interactions between cells in the tumor microenvironment (TME) shape cancer progression and patient outcomes. To gain new insights into how the TME influences cancer outcomes, we derive gene expression signatures indicative of signaling between stromal fibroblasts and cancer cells, and demonstrate their prognostic significance in multiple and independent squamous cell carcinoma cohorts. By leveraging information within the signatures, we discover that the HB-EGF/EGFR/MEK axis represents a hub of tumor - stroma crosstalk, promoting the expression of CSF2 and LIF and favoring the recruitment of macrophages. Together these analyses demonstrate the utility of our approach for interrogating the extent and consequences of TME crosstalk.

cancer biology↗

bioRxiv2021

Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma

Cancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organized in a variety of ways, ranging from thin discontinuous strands to thick pushing collectives. Here we employ an integrated experimental and computational approach to identify the factors that determine the mode of collective cancer cell invasion. We find that matrix proteolysis is linked to the formation of wide strands, but has little effect on the maximum extent of invasion. Cell-cell junctions also favour wide strands, but our analysis also reveals a requirement for cell-cell junctions for efficient invasion in response to uniform directional cues. Unexpectedly, the ability to generate wide invasive strands is coupled to the ability to grow effectively when surrounded by ECM in 3D assays. Combinatorial perturbation of both matrix proteolysis and cell-cell adhesion demonstrates that the most aggressive cancer behaviour, both in terms of invasion and growth, is achieved at high levels of cell-cell adhesion and high levels of proteolysis. Contrary to expectation, cells with canonical mesenchymal traits - no cell-cell junctions and high proteolysis - exhibit reduced growth and lymph node metastasis. Thus, we conclude that the ability of squamous cell carcinoma cells to invade effectively is also linked to their ability to generate space for proliferation in confined contexts. These data provide an explanation for the apparent advantage of retaining cell-cell junctions in SCC.

cancer biology↗

bioRxiv2020

EphB6 regulates TFEB-lysosomal pathway and survival of disseminated indolent breast cancer cells

Late relapse of disseminated cancer cells is a common feature of some types of tumors. Several intrinsic and extrinsic factors have been shown to affect reawakening of disseminated dormant cancer cells (DDCCs); however, the signals and processes sustaining survival of DDCCs in a foreign environment are still poorly understood. We have recently shown that crosstalk with lung epithelial cells promotes persistence of DDCCs from estrogen receptor positive (ER+) breast tumors. Here we show that TFEB-lysosomal axis is activated in DDCCs and that it is modulated by the pro-survival ephrin receptor EphB6. TFEB lysosomal direct targets are enriched in DDCCs in vivo and correlate with relapse in ER+ breast cancer patients. Direct contact of DDCCs with alveolar type I-like lung epithelial cells drives lysosomal accumulation and EphB6 induction. EphB6 contributes to TFEB transcriptional activity and lysosome formation in DDCCs in vitro and in vivo, and supports survival of DDCCs in coculture and in vivo. Furthermore, signaling from EphB6 promotes the proliferative response of surrounding lung parenchymal cells in vivo.

cancer biology↗