Biology subjects

Cooke, S.

Publications and source records attributed to Cooke, S..

7 recordsLinked to original sources

bioRxiv2026

Arabidopsis GHL1 is an orthologue of Hedgehog acyl transferase but likely catalyses GPI-anchor remodelling rather than peptide acylation.

The GUP1/HHAT family of MBOAT proteins have been implicated in GPI-anchor acyl-chain remodelling in fungi and secreted peptide acylation in eumetazoans, but whether these activities are distinct or GUP1/HHAT proteins are bifunctional has not been addressed. We show that the GUP1/HHAT family form a distinct orthologous clade within eukaryotes with structural homology, suggesting a single evolutionary event for their origin and common mode of action. Arabidopsis plants homozygous for loss of GUP1/HHAT-like activity cannot be recovered suggesting that loss is lethal, and further examination suggests that there are severe effects on transmission through the male gamete. Recent work suggests that rice GUP1-like BC16 is a GPI-anchor acyl-chain remodelase, but a potential role for non-eumetazoan GUP1 and HHAT-like proteins in secreted peptide acylation has not been assessed. By reconstituting HHAT peptide acyl transferase activity towards Hedgehog-like peptides in plants we demonstrate that Arabidopsis GUP1/HHAT-like proteins likely do not possess appreciable HHAT-like peptide acyltransferase activity. However, through this work we provide a novel means for cell surface display of proteins in eukaryotic systems, demonstrating that the minimal acyl-acceptor peptide sequence of Hedgehog morphogens, when expressed alongside HHAT, allows for immobilisation of proteins in the outer leaflet of the plasma membrane via their N-terminus, rather than the C-terminus as is the case for traditional GPI-anchor mediated cell surface display.

plant biology↗

bioRxiv2025

Androgen receptor inhibition extends PARP inhibitor activity in prostate cancer models beyond BRCA mutations and defects in homologous recombination repair.

Recent phase 3 clinical trial readouts have shown benefit of the combination of poly(ADP-ribose) polymerase inhibitors (PARPi) with androgen receptor (AR) pathway inhibitors (ARPi) in metastatic, castration-resistant prostate cancer (mCRPC). While benefit was particularly evident in patients with tumours harbouring mutations in homologous recombination repair (HRR) genes, improved outcomes were also observed in patients with no such defined alterations in their cancers. Although there is literature linking AR activity with DNA repair pathways, the basis of the interaction between the AR and PARP is unclear. Here, we show that benefit of the combination of ARPi and PARPi in prostate cancer in vitro and in vivo models with no HRR mutations requires ARPi-responsive cells and a PARPi with PARP1-trapping activity, and does not involve an effect of PARPi treatment in modulating the transcriptional role of the AR. Combination benefit is driven by an increase in DNA damage in the form of DNA double-strand breaks and micronuclei formation, which is not due to a direct control of HRR gene transcription by the AR. In addition, we uncover a novel role of PARP1 in modulating AR recruitment to chromatin in the presence of DNA damage. These data shed new light on the interplay between PARP1 and the AR in dealing with genotoxic insults and provide a mechanism of action consistent with the observed clinical benefit of the combination of PARPi and ARPi in patients with prostate cancer. Statement of significanceCombination of androgen receptor pathway inhibitors and PARP inhibitors has shown efficacy in prostate cancer. We provide a mechanistic explanation through increased DNA damage accumulation observed in combination vs single-agent treatments.

cancer biology↗

bioRxiv2022

A role for thalamic projection GABAergic neurons in circadian responses to light

The thalamus is an important hub for sensory information and participates in sensory perception, regulation of attention, arousal and sleep. These functions are executed primarily by glutamatergic thalamocortical neurons that extend axons to the cortex and initiate cortico-thalamocortical connectional loops. However, the thalamus also contains projection GABAergic neurons that do not engage in direct communication with the cortex. Here, we have harnessed recent insight into the development of the intergeniculate (IGL), the ventrolateral geniculate (LGv) and the perihabenula (pHB) to specifically target and manipulate thalamic projection GABAergic neurons in female and male mice. Our results show that thalamic GABAergic neurons of the IGL and LGv receive retinal input from diverse classes of ipRGCs, but not from the M1 ipRGC type, while those in the pHB lack direct retinal input. We describe the synergistic role of the photoreceptor melanopsin and the thalamic neurons of the IGL/LGv in circadian entrainment to dim light. We identify a requirement for the thalamic IGL/LGv in the rapid changes in vigilance states associated with circadian light transitions. Furthermore, we map a previously undescribed thalamic network of developmentally related GABAergic neurons in the IGL/LGv complex and the pHB potentially involved in light-dependent mood regulation. Significance statementThe intergeniculate leaflet and ventral geniculate nucleus are part of the extended circadian system and mediate some non-image-forming visual functions. Here we show that each of these structures has a thalamic (dorsal) as well as prethalamic (ventral) developmental origin. We map the retinal input to thalamus-derived cells in the IGL/LGv complex and discover that while ipRGC input is dominant, this is not likely to originate from M1-ipRGCs. We describe the extent of similarity in synaptic input to developmentally related cells in the IGL/LGv and in the perihabenula nucleus (pHB). We implicate thalamic cells in the IGL/LGv in vigilance state transitions at circadian light changes and in overt behavioural entrainment to dim light, the latter exacerbated by concomitant loss of melanopsin expression.

neuroscience↗

bioRxiv2021

Dispersed Sleep Microstates and Associated Structural Changes in GBA1 Mouse: Relevance to Rapid Eye Movement Behavior Disorder

Rapid eye movement (REM) sleep behaviour disorder (RBD) is a rare parasomnia that may predict the later occurrence of alpha-synucleinopathies. Variants in the gene encoding for the lysosomal enzyme glucocerebrosidase, GBA, strongly increase the risk of RBD. In a GBA1-mouse model recently shown to mimic prodromal stages of -synucleinopathy, we now demonstrate striking REM and NREM sleep abnormalities accompanied by distinct structural changes in the more widespread sleep neurocircuitry.

neuroscience↗

bioRxiv2020

Ovarian carcinosarcoma genomics and pre-clinical models highlight the N-MYC pathway as a key driver and susceptibility to EMT-targeting therapy

Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory from a single progenitor, resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). We show OCS from 18 women to be monoclonal through analysis of DNA variants from isolated carcinoma and sarcoma components. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure ovarian carcinomas, supporting the conversion theory. We used pre-clinical OCS models to test the efficacy of microtubule-targeting drugs, including eribulin, which has been shown to reverse EMT characteristics. We demonstrated that microtubule inhibitors, vinorelbine and eribulin, were more effective than standard-of-care platinum-based chemotherapy. Eribulin reduced mesenchymal characteristics, N-MYC expression and cholesterol biosynthesis. Finally, eribulin induced a strong immune response, supporting immunotherapy combinations in the clinic.

cancer biology↗

bioRxiv2019

The right temporoparietal junction is causally associated with embodied perspective taking

Several theories exist pertaining to the role of the right temporoparietal junction (rTPJ) in social cognition. A prominent theory claims the rTPJ is especially associated with embodied processes. In the present study we use high-definition transcranial direct current stimulation (HD-tDCS) to provide evidence that the rTPJ is causally associated with the embodied processes underpinning perspective taking. Eighty-eight young human adults were stratified to receive either rTPJ or dorsomedial prefrontal (dmPFC) anodal HD-tDCS in a sham-controlled, double-blind, repeated-measures design. Perspective tracking (line-of-sight) and perspective taking (embodied rotation) were assessed using a visuo-spatial perspective taking (VPT) task that required understanding what another person could see or how they see it, respectively. Embodied processing was manipulated by positioning the participant in a manner congruent or incongruent with the orientation of an avatar on the screen. As perspective taking, but not perspective tracking, is influenced by bodily posture, this allows the investigation of the specific causal role for the rTPJ in embodied processing. Crucially, anodal stimulation to the rTPJ increased the effect of bodily posture during perspective taking, whereas no such effects were identified during perspective tracking, thereby providing evidence for a causal role for the rTPJ in the embodied component of perspective taking. Stimulation to the dmPFC had no effect on perspective tracking or taking. Therefore, the present study provides support for theories postulating that the rTPJ is causally involved in embodied cognitive processing relevant to social functioning.\n\nSignificance StatementThe ability to understand anothers perspective is a fundamental component of social functioning. Adopting another perspective is thought to involve both embodied and non-embodied processes. The present study used high-definition transcranial direct current stimulation (HD-tDCS) and provided causal evidence that the right temporoparietal junction (rTPJ) is involved specifically in the embodied component of perspective taking. Specifically, HD-tDCS to the rTPJ, but not another hub of the social brain (dmPFC), increased the effect of body posture during perspective taking, but not tracking. This is the first causal evidence that HD-tDCS can modulate social embodied processing in a site-specific and task-specific manner.

neuroscience↗

bioRxiv2017

Epigenetic maintenance of DNA methylation after evolutionary loss of the de novo methyltransferase

Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles, yet has been lost many times in diverse eukaryotic lineages. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase, Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 MYA. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 MY through a process analogous to Darwinian evolution of the genome.

molecular biology↗