Biology subjects

Sharp, A.

Publications and source records attributed to Sharp, A..

10 recordsLinked to original sources

bioRxiv2025

ProMPt: A modular preclinical platform for functional modelling of prostate cancer heterogeneity and therapeutic vulnerabilities

Prostate cancer progression is driven by heterogenous genetic, phenotypic, and microenvironmental programs that remain challenging to model experimentally. Existing systems such as genetically engineered mouse models, xenografts, and patient-derived organoids have each advanced mechanistic insight but are limited by genetic scope, scalability, or lack of immune context. To overcome these constraints we developed ProMPt, a genetically-defined syngeneic mouse modelling platform that captures combinations of the most recurrent clinical prostate cancer genomic alterations to enable scalable in vitro and in vivo interrogation of prostate cancer evolution. Tumours derived from ProMPt organoids recapitulate the histologic and molecular diversity of human disease. Cross - species transcriptomic integration and multivariate single-cell analysis under defined culture permutations revealed conserved phenoscapes, highlighting a central role for MYC in disease progression and therapy resistance. Guided by these insights, preclinical intervention studies demonstrated that combined MAPK inhibition and blockade of protein translation synergistically suppressed tumour growth in castration-resistant models. This combination not only suppressed proliferation but also remodelled the tumour immune landscape, underscoring its dual epithelial and microenvironmental effects. Together, these findings establish ProMPt as a versatile framework for linking genotype, lineage plasticity, and therapeutic vulnerability in prostate cancer.

cancer biology↗

bioRxiv2025

Stand age drives changes in the biodiversity and microclimate of oil palm plantations

Tree plantation age strongly dictates its environment. As they mature, the canopy closes and habitat complexity tends to increase, which in turn affects biodiversity. However, for oil palm, one of the most important and widespread tree plantations, we lack a detailed understanding of how this process affects microclimate and biodiversity. We therefore compiled environmental and biodiversity data of oil palm plantations that were repeatedly sampled over a 6 year period in Malaysian Borneo. Using these data, we made a chronosequence of the microclimate and biodiversity of oil palm plantations between the ages 5 and 18. We found that oil palm plantations increasingly buffer temperature and humidity over time, becoming cooler and less dry. Animal responses differed between taxa: spider and beetle abundance increased, ant abundance decreased, and mammal and dung-beetle abundances stayed constant. The diversity of beetles in general increased and family-level community composition changed, while dung-beetle and mammal diversity stayed constant. Some taxa are therefore likely limited by the harsh microclimate of young plantations, while increased habitat complexity and fruit and leaf production in older plantations could also drive increased abundances of other taxa. Our results reveal that oil palm plantations undergo considerable changes, even over a decade after establishment. Correspondingly, plantation age should be considered in studies into oil palm plantations impact on climate and biodiversity, and landscape level diversity could be increased by allowing multiple oil palm stand-ages to co-exist.

ecology↗

bioRxiv2024

MyVivarium: A cloud-based lab animal colony management application with near-realtime ambient sensing

Management of research-animal colonies is vital for lab productivity in preclinical research. Labs often rely on inefficient paper-based or spreadsheet-based methods to manage animal colonies. Dedicated software-based solutions are generally expensive and many lack remote access. Currently available open-source alternatives are difficult to implement and deploy. These solutions also do not have the capability to track ambient variables that affect colony well-being. We built MyVivarium, an open-source database management web application to address these gaps. MyVivarium can be easily deployed to the cloud and sustained for a cost comparable to starting and maintaining a lab website. Using MyVivarium, lab members can collaboratively track individual animals within a database. Physical identities of cages map onto the database using QR codes, enabling quick and easy record-keeping on mobile devices. Lab administrators can assign tasks to users with reminders for experiments or cage maintenance. Finally, we designed a low-cost system to sense ambient humidity, temperature, vivarium worker activity, and room illuminance. These data are then sent to MyVivarium in realtime providing information relevant to colony well-being. Taken together, MyVivarium is a novel, open-source, cloud-based application template that provides a low-cost, simple, and efficient way to digitally manage research-animal colonies.

bioinformatics↗

bioRxiv2024

AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer

Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.

cancer biology↗

bioRxiv2022

Targeting the BAG-1 family of co-chaperones in lethal prostate cancer.

Therapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR drives transcriptional activity in CRPC but is intrinsically disordered and remains a challenging therapeutic target. Therefore, inhibiting critical co-chaperones, such as BAG-1L, is an attractive alternative strategy. We performed druggability analyses demonstrating the BAG domain to be a challenging drug target. Thio-2, a tool compound, has been reported to bind the BAG domain of BAG-1L and inhibit BAG-1L-mediated AR transactivation. However, despite these data, the mechanism of action of Thio-2 is poorly understood and the BAG domain which is present in all BAG-1 isoforms has not been validated as a therapeutic target. Herein, we demonstrate growth inhibiting activity of Thio-2 in CRPC cell lines and patient derived models with decreased AR genomic binding and AR signaling independent of BAG-1 isoform function. Furthermore, genomic abrogation of BAG-1 isoforms did not recapitulate the described Thio-2 phenotype, and NMR studies suggest that Thio-2 may bind the AR NTD, uncovering a potential alternative mechanism of action, although in the context of low compound solubility. Furthermore, BAG-1 isoform knockout mice are viable and fertile, in contrast to previous studies, and when crossed with prostate cancer mouse models, BAG-1 deletion does not significantly impact prostate cancer development and growth. Overall, these data demonstrate that Thio-2 inhibits AR signaling and growth in CRPC independent of BAG-1 isoforms, and unlike previous studies of the activated AR, therapeutic targeting of the BAG domain requires further validation before being considered a therapeutic strategy for the treatment of CRPC.

molecular biology↗

bioRxiv2021

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

BackgroundMost animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false positive signals. ResultsWe generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30-40 times using HiFi sequencing is required for phasing of the leaf rust genome (~0.7% heterozygosity) and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. ConclusionsThis first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.

genomics↗

bioRxiv2020

Episignatures stratifying ADNP syndrome show modest correlation with phenotype

ADNP syndrome, also known as Helsmoortel-van Der Aa syndrome, is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. ADNP syndrome is caused by mutations in the activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with ADNP syndrome, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with ADNP syndrome into two groups, based on the location of the mutations. Here, we conducted an independent study on 24 individuals with ADNP syndrome and replicated the existence of the two, mutation-dependent ADNP episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of ADNP syndrome. We found limited phenotypic differences between the two ADNP groups, and no evidence that individuals with more widespread methylation changes are more severely affected. Also, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with ADNP syndrome. Our data warrant caution in harnessing methylation signatures in ADNP syndrome as a tool for clinical stratification, at least with regards to behavioral phenotypes.

developmental biology↗

bioRxiv2019

Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats

BackgroundWithin-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses - particularly those produced through mastication of tough food items - may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, shape variation should not be dominated by allometry; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues.\n\nResultsWe assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of thre species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus.\n\nDiscussionOur results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraint act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.

evolutionary biology↗

bioRxiv2018

Forest quality, forest area and the importance of beta-diversity for protecting Borneo’s beetle biodiversity

The lowland forest of Borneo is threatened by rapid logging for timber export and clearing for the expansion of timber and oil palm plantations. This combination of processes leaves behind landscapes dotted with small, often heavily-degraded forest fragments. The biodiversity value of such fragments, which are easily dismissed as worthless, is uncertain. We collected 187 taxa of rove beetles across a land-use gradient in Sabah, Malaysia, spanning pristine tropical lowland forest to heavily-degraded forest. Using these data, we identified shifts in alpha-, beta-, and gamma-diversity in response to forest quality and distance, then applied our findings from continuous expanses of forest to make predictions on hypothetical forest areas. We found that maintaining high forest quality is more important than forest area for conserving rare taxa (those important for conserving biodiversity per se), and that very small areas (10 ha) are likely to harbour the same richness of rove beetles as larger areas (100 ha) of equal forest quality. We estimate a decline in richness of 36% following heavy logging (removal of 95% of the vegetation biomass) from a forest area of 100 ha or less. Maintaining large forest area as well as high forest quality is important for conserving community composition, likely to be more important for conserving ecosystem functioning. We predict a decline of 35% in community diversity in conversion of a 100 ha area of unlogged forest to a 10 ha area of heavily-logged forest. Despite significant declines in alpha-diversity, beta-diversity within small rainforest areas may partially mitigate the loss of gamma-diversity, reinforcing the concept that beta-diversity is a dominant force determining the conservation of species in fragmented landscapes. In contrast to previous findings on larger animals, our results suggest that even small fragments of degraded forest might be important reservoirs of invertebrate biodiversity in tropical agriculture landscapes. These fragments, especially of lightly-logged forest, should be conserved where they occur and form an integral part of management for more sustainable agriculture in tropical landscapes.

ecology↗

bioRxiv2018

Identification of rare de novo epigenetic variations in congenital disorders

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. With recent dramatic advances in genomic technologies, genome-wide surveys of cohorts of patients with ND/CAs for point mutations and structural variations have greatly advanced our understanding of their genetic etiologies1,2. However, even after whole genome sequencing (WGS), a substantial fraction of such disorders remain unexplained3. In contrast, the possibility that constitutive epigenetic variations (epivariations) might underlie such traits has not been well explored. We hypothesized that some cases of ND/CA are caused by aberrations of DNA methylation that lead to a dysregulation of normal genome function. By comparing DNA methylation profiles from 489 individuals with ND/CAs against 1,534 population controls, we identified epivariations as a frequent occurrence in the human genome. De novo epivariations were significantly enriched in cases when compared to controls. RNAseq data from population studies showed that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detected and replicated an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations. Thus, some epivariations occur secondary to cis-linked mutations in regulatory regions, providing a rationale for interpreting non-coding genetic variation. We propose that epivariations likely represent the causative genomic defect in 5-10% of patients with unexplained ND/CAs. This constitutes a yield comparable to CNV microarrays, and as such has significant diagnostic relevance.

genomics↗