Biology subjects

Brooke, G. N.

Publications and source records attributed to Brooke, G. N..

8 recordsLinked to original sources

bioRxiv2025

MSC-delivered High-Affinity Variants of soluble PD1 lead to tumour regression

Immune checkpoint therapies aim to restore anti-tumour immunity by blocking inhibitory signals that suppress T-cell activation. The most effective current strategies use humanised antibodies targeting PD1 or its ligand PDL1. However, due to their large size, antibodies often exhibit limited tissue diffusion, resulting in poor penetration into solid tumours. To address this challenge, we developed a novel checkpoint inhibitor approach that uses mesenchymal stromal cells (MSCs) to deliver a high-affinity, soluble PD1 receptor (sPD1HAC). We found that sPD1HAC produced as an IgG1-Fc fusion protein provided functional expression in MSCs. The sPD1HAC-IgG1-Fc fusion protein showed strong and specific binding to PDL1 and could outcompete recombinant PD1 and anti-PDL1 antibodies, including the clinically approved durvalumab. Although the sPD1HAC variant was designed to block human PD1-PDL1 signalling, it also bound murine PDL1 and blocked the binding of mouse-specific PD1 antibodies as well as recombinant murine PD1 protein. Accordingly, we found significant anti-tumour activity of intravenously administered MSCs.PD1HAC in an aggressive B16-F10 cancer model. This cell-based immune checkpoint approach offers a potential therapeutic option for targeting stroma-rich, treatment-resistant tumours.

cancer biology↗

bioRxiv2025

Reliable repurposing of antibody interactome inside the cell

In biology proximity is paramount and eighty-five percent of the human proteome has at least one documented interacting monoclonal antibody. These molecules penetrate the cytoplasm poorly and are very often non-functional within the cell. Sequence analysis of 106 antibody variable domains alongside the cytoplasmic human proteome shows charge and isoelectric point are characteristics ill adapted to intracellular monodispersity. Characterisation of forty-five single-chain variable fragment (scFv) intrabodies expressed in human cells confirmed charge to have the greatest impact on solubility. We created new interdomain linkers, optimised scFv domain orientation and found variable heavy domain framework sites to be generally positively charged, and promote insolubility, but be amenable to optimisation. This is applied in combination to reduce the search space and refine the products of AI-led inverse folding to create highly soluble, abundant and thermally stable intrabodies that maintain parent antibody epitope recognition. Over six hundred intrabody sequences are described targeting sixty cytoplasmic proteins with linear, conformational, post-translational modification or oligomeric state specificity. Interactions were validated for p53, -synuclein, SOD1, polyQ, FUS/TLS, UCHL1 and GFP. This approach removes obstacles hindering intracellular repurposing of the vast sequenced antibody interactome with applications relevant to many human disease states.

molecular biology↗

bioRxiv2024

Analysis of coding gene expression from small RNA sequencing

The popularity of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies where matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA-gene regulatory networks. We explore whether protein-coding gene expression can be quantified directly from transcript fragments present in sRNA-seq experiments. We analyze studies containing matched total RNA and small RNA from four human tissues and recover transcript fragments from the sRNA-seq datasets. We find that the expression levels of protein-coding gene transcripts derived from sRNA-seq datasets are comparable to those from total RNA-seq experiments (R2 ranging from 0.33 to 0.76). Analyses across multiple tissues and species show similar correlations, indicating that the approach is applicable across organisms. We confirm that transcript half-life and the expression of housekeeping or highly abundant genes do not bias the results. Analysis of the expression of both microRNAs and coding genes from the same sRNA-seq experiments demonstrate that known microRNA-target interactions are, as expected, inversely correlated with the expression profiles of these microRNA-mRNA pairs. For a dual mRNA/miRNA profile, we recommend sequencing the [≥]25 nucleotide fraction at [≥] 5 M reads. To confirm the utility of this approach, we apply our method to breast cancer sRNA-seq datasets lacking total RNA-seq data and achieve 75% recall and 64% accuracy comparing inferred coding gene expression with qPCR-validated targets. Our findings demonstrate that quantifying mRNA fragments from sRNA-seq experiments provides a reliable approach to investigate microRNA-mRNA interactions when total RNA-seq is unavailable.

genomics↗

bioRxiv2024

The p90 Ribosomal S6 Kinases 2 and 4 promote Prostate Cancer cell proliferation in androgen-dependent and independent ways

Oncogenic activation of the phosphatidylinositol-3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways are frequent events in Prostate Cancer (PCa) that have been correlated to tumour formation, disease progression and therapeutic resistance. At the intersection of these two pathways lies the p90 ribosomal S6 kinase (RSKs) family, which regulates many proteins involved in cell survival, growth and proliferation. As such, deregulated RSKs activity has been associated with multiple cancer types, including PCa. However, the full extent of the RSKs involvement in prostate tumorigenesis remains to be determined. Here we have shown that RSKs levels are increased in PCa samples and cell lines. The RSKs were found to enhance Androgen Receptor (AR) activity, the key oncogenic driver in PCa. Indeed, all RSKs were found to interact in close proximity to the AR. However, RSK2/4, but not RSK1/3, showed changes in cell localisation following AR nuclear translocation. Consistently, silencing of RSK2/4, but not RSK1/3, inhibited PCa proliferation in an androgen-dependent and independent manner, respectively, and induced different signaling events downstream of the AR. The data suggests that RSK2 and RSK4 activity is required for PCa cell proliferation, but they are likely regulating growth via different mechanisms.

cancer biology↗

bioRxiv2024

A novel glutathione peroxidase-based biosensor disentangles differential subcellular accumulation of H2O2 and lipid hydroperoxides

Hydrogen peroxide (H2O2) and lipid hydroperoxides (LOOH) are initiators and transducers of inter- and intra-cellular signaling in response to diverse environmental, pathological and developmental cues. The accumulation of both H2O2 and LOOH is often temporally and spatially coincident in tissues, but it is unknown if this coincidence extends to subcellular compartments. If distinct accumulation of different peroxides occurs at this smaller spatial scale, then it would be an important factor in signaling specificity. Fusion of the redox-sensitive (ro)GFP2 to the Saccharomyces cerevisiae (yeast) OXIDANT RECEPTOR PEROXIDASE1 (ORP1), also known as GLUTATHIONE PEROXIDASE3 (GPX3), created a now widely used biosensor that is assumed to detect H2O2 in vivo. This is despite monomeric GPX enzymes, such as ORP1/GPX3, possessing wide peroxide substrate specificities. Consequently, we confirmed in vitro that roGFP2-ORP1 is not only oxidized by H2O2, but also by phospholipid fatty acid peroxides generated in lecithin-derived liposomes by lipoxygenase-catalyzed peroxidation. This led us to doubt that roGFP2-ORP1 in vivo is specific for H2O2. To address this issue of peroxide specificity, we constructed a modified biosensor called roGFP2-synORP1. This version has greatly diminished reactivity towards phospholipid fatty acid peroxides but retains high sensitivity for H2O2. These two roGFP2-based biosensors, targeted to chloroplasts, cytosol and the nucleus, were quantitatively imaged in parallel in Nicotiana benthamiana abaxial epidermal cells experiencing high light- and herbicide-induced photo-oxidative stress. From differential patterns of oxidation of these probes, we inferred that the chloroplasts accumulated both peroxide types. In contrast, LOOH and H2O2 accumulated exclusively in the cytosol and nucleus respectively. Therefore, this suggests that the signalling networks initiated by different peroxides will have a distinct spatial component.

molecular biology↗

bioRxiv2023

The antiviral potential of the antiandrogen enzalutamide and the viral-androgen interplay in seasonal coronaviruses

The sex disparity in COVID-19 outcomes with males generally faring worse than females has been associated with the androgen-regulated expression of the protease TMPRSS2 and the cell receptor ACE2 in the lung and fueled interest in antiandrogens as potential antivirals. In this study, we explored enzalutamide, an antiandrogen used commonly against prostate cancer, as a potential antiviral against the human coronaviruses which cause seasonal respiratory infections (HCoV-NL63, -229E, and -OC43). Using lentivirus-pseudotyped and authentic HCoV, we report that enzalutamide reduced 229E and NL63 entry and replication in both TMPRSS2- and non-expressing immortalised cells, suggesting a TMPRSS2-independent mechanism. However, no effect was observed against OC43. To decipher this distinction, we performed RNA-sequencing analysis on 229E-and OC43- infected primary human airway cells. Our results show a significant induction of androgen-responsive genes by 229E compared to OC43 at 24 and 72h post-infection. The virus-mediated effect to AR signaling was further confirmed with a consensus androgen response element (ARE)-driven luciferase assay in androgen-depleted MRC-5 cells. Specifically, 229E induced luciferase reporter activity in the presence and absence of the synthetic androgen mibolerone, while OC43 inhibited induction. These findings highlight a complex interplay between viral infections and androgen signaling, offering insights for potential antiviral interventions.

microbiology↗

bioRxiv2023

Nucleosome reorganisation in breast cancer tissues

Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. Here we have generated high resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with [~]20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. In addition, tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. These effects were correlated with gene activity, DNA sequence repeats abundance, differential DNA methylation and binding of linker histone variants H1.4 and H1X. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient stratification and monitoring using liquid biopsies.

genomics↗

bioRxiv2020

Fas-threshold signalling in MSCs causes tumour progression and metastasis

Mesenchymal stem cells (MSCs) are part of the tumour microenvironment and have been implicated in tumour progression. We found the number of MSCs significantly increased in tumour-burdened mice driven by Fas-threshold signalling. Consequently, MSCs lacking Fas lost their ability to induce metastasis development in a pancreatic cancer model. Mixing of MSCs with pancreatic cancer cells led to sustained production of the pro-metastatic cytokines CCL2 and IL6 by the stem cells. The levels of these cytokines depended on the number of MSCs, linking Fas-mediated MSC-proliferation to their capacity to promote tumour progression. Furthermore, we discovered that CCL2 and IL6 were induced by pancreatic cancer cell-derived IL1. Analysis of patient transcriptomic data revealed that high FasL expression correlates with high levels of MSC markers as well as increased IL6 and CCL2 in pancreatic tumours. Moreover, both FasL and CCL2 are linked to elevated levels of markers specific for monocytes known to possess further pro-metastatic activities. These results confirm our experimental findings of a FasL-MSC-IL1-CCL2/IL6 axis in pancreatic cancer and highlight the role MSCs play in tumour progression.

cancer biology↗