Biology subjects

Burke, E.

Publications and source records attributed to Burke, E..

5 recordsLinked to original sources

bioRxiv2026

Pharmacological targeting of EED is an effective therapeutic strategy in cellular models of incurable neuroendocrine prostate cancer

BackgroundNeuroendocrine Prostate Cancer (NEPC) is an incurable malignancy, originating from the trans-differentiation of prostate adenocarcinoma (PRAD). Compared to PRAD, NEPC shows over-activation of Polycomb Repressive complex-1(PRC1) and-2 (PRC2), which are multiprotein epigenetic writers that drive cancer progression via tumour suppressor gene silencing. Tazemetostat is a PRC2 inhibitor approved for the treatment of sarcomas and lymphomas. ORIC-944 is a novel EED (Embryonic Ectoderm Development) inhibitor, which is being tested in clinical trials. EED is an attractive target as it functions as a key component of both PRC1 and PRC2. Objective and MethodsWe compared the anticancer effects of tazemetostat and ORIC-944 in NEPC and PRAD cells. Cells were exposed to various concentrations of the two compounds to measure effects on cell viability (IC50) and apoptosis (flow cytometry). PRC2 inhibition was confirmed by measuring histone H3 Lys 27 trimethylation (H3K27me3) via ELISA and Western Blot. RNA Sequencing and pathway analysis was conducted to study modes of actions of tazemetostat vs ORIC-944. ResultsUnlike tazemetostat, ORIC-944 causes dose-dependent growth inhibition in both NEPC and PRAD cells. In this context, EED targeting achieves IC50 values that are comparable to those of compounds used for the clinical treatment of advanced prostate cancer. Moreover, ORIC-944 (but not tazemetostat) causes significant apoptosis in NEPC cells. Both tazemetostat and ORIC-944 reduce H3K27me3. Mechanistically, both compounds reactivate the expression of known PRC2 targets, such as genes that control neural differentiation. However, the EED inhibitor also reactivates PRC1 targets, including pro-apoptotic and anti-proliferating genes (e.g. metallothionines). This evidence suggests that EED inhibition is a promising therapeutic strategy for NEPC.

cancer biology↗

bioRxiv2025

The Polycistronic Transcription Landscape of the Populus Genome

Transcripts spanning multiple gene loci are common in prokaryotes as a feature of polycistronic gene expression but have traditionally been considered rare in eukaryotic nuclear genomes. In this study, using Nanopore direct RNA sequencing (DRS), we identified widespread mRNA transcripts spanning two or more nuclear gene loci in two Populus species, Populus trichocarpa (Nisqually-1) and the hybrid poplar 717 (P. tremula x P. alba). These novel multi-gene-spanning transcripts structurally resemble polycistronic RNAs and are predicted to encode open reading frames (ORFs), including modified and fusion ORFs. Many of these transcripts exhibit tissue-specific, allele-specific, or drought-responsive expression pattern, suggesting potential roles in plant development and environmental adaptation. Functional enrichment and protein localization analyses revealed that genes associated with organelles and membranes are significantly overrepresented within these polycistronic-like (PC-like) transcriptional units. PC-like RNAs also undergo extensive alternative splicing and possess longer polyadenine [poly(A)] tails and fewer N-methyladenosine (mA) modification sites than their monocistronic counterparts. Under drought, dicistronic-like RNAs were more strongly coregulated with the corresponding 5' monocistronic gene than with the 3' monocistronic gene, whereas the two corresponding monocistronic genes exhibited a weaker positive correlation in expression. These findings indicate that transcription and RNA processing at PC-like loci are regulated through mechanisms distinct from those governing prokaryotic polycistronic operons. Collectively, our results reveal pervasive PC-like transcription in plant nuclear genomes and highlight its distinctive molecular features, complex regulation, and potential roles in plant growth and environmental adaptation.

genomics↗

bioRxiv2024

Efficient 3'-end tailing of RNA with modified adenosine for nanopore direct total RNA sequencing

Direct sequencing of total cellular RNA enables a better understanding of a broad spectrum of RNA species controlling cellular processes and organismal function. Current nanopore direct RNA sequencing method, however, only captures polyadenylated RNA for sequencing. To address this issue, we developed a unique 3-end RNA tailing method to capture total RNA for nanopore direct RNA sequencing. Due to the distinct electrical signature of the added tail on nanopore, this method allows simultaneous detection of both non-polyadenylated and polyadenylated RNAs. We demonstrated the effectiveness of this method in capturing the dynamics of transcription and polyadenylation of chloroplast RNAs in plant cell. With its high efficiency in retaining total RNA on nanopore, this method has the potential to be broadly applied to RNA metabolism and functional genomics studies.

genomics↗

bioRxiv2020

Functional modeling of NMIHBA-causing PRUNE1 variants reveals a requirement for its exopolyphosphatase activity.

Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G>A (p.Arg128Gln), c.520G>T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment.

genetics↗

bioRxiv2018

Target specific routing of visual information by the superior colliculus

Using sensory information to trigger different behaviours relies on circuits that pass-through brain regions. However, the rules by which parallel inputs are routed to different downstream targets is poorly understood. The superior colliculus mediates a set of innate behaviours, receiving input from ~30 retinal ganglion cell types and projecting to behaviourally important targets including the pulvinar and parabigeminal nucleus. Combining transsynaptic circuit tracing with in-vivo and ex-vivo electrophysiological recordings we observed a projection specific logic where each collicular output pathway sampled a distinct set of retinal inputs. Neurons projecting to the pulvinar or parabigeminal nucleus uniquely sampled 4 and 7 cell types, respectively. Four others innervated both pathways. The visual response properties of retinal ganglion cells correlated well with those of their disynaptic targets. These findings suggest that projection specific sampling of retinal inputs forms a mechanistic basis for the selective triggering of visually guided behaviours by the superior colliculus.

neuroscience↗