Biology subjects

Cheung, D.

Publications and source records attributed to Cheung, D..

5 recordsLinked to original sources

bioRxiv2025

A synaptic-astrocytic proteomic signature associated with synaptopathy in Alzheimer's Disease

Synapse loss is the greatest correlate of cognitive impairment in Alzheimers Disease (AD) and offers a therapeutic avenue alongside disease-modifying therapies. However, the events preceding synapse loss in the human condition have not been well characterised. In this study, we describe a pseudotemporal profile of alterations in the synaptic proteome prior to excitatory synapse loss in human post-mortem brain AD tissue using synapse proteomics and synaptome mapping techniques. In a region with early-stage disease pathology, the most predominant changes were pre-synaptic and featured changes in metabolism and exocytosis. In a mid-stage disease state, alongside initial synapse loss, there was a dominance of inhibitory synaptic changes. In a region with late-stage disease pathology and profound synapse loss, post-synaptic changes were most prevalent with a range of canonical synaptic transmission pathways reduced and differential excitatory synapse subtype pathology. Synapse loss was associated with changes in astrocytic proteins which were enriched for those at peri-synaptic astrocytic processes, including an upregulation of complement activation and endocytosis; a signature that differed from the astrocyte cytosolic proteome. Taken together, this provides evidence of a cascade of events leading to synapse loss with multiple points for therapeutic intervention to alleviate cognitive decline in AD. Data are available via ProteomeXchange with identifier PXD056052.

neuroscience↗

bioRxiv2024

Practical Media Formulations for Rapid Growth of Lactobacillus iners and Other Vaginal Bacteria

Vaginal microbiome composition is closely tied to host health. A microbiome dominated by specific anaerobes (e.g., Gardnerella vaginalis) is termed bacterial vaginosis (BV) and is associated with negative health outcomes, while colonization by Lactobacillus species is thought to protect against BV. However, the role of the species Lactobacillus iners in vaginal health is controversial, with evidence that some strains may not protect against BV while others do. To better characterize L. iners strains, their interactions with vaginal bacteria and human cells need to be investigated in vitro, but this has been impeded by the lack of liquid media for rapid L. iners growth. We have developed three liquid media formulations for L. iners growth: Serradors Lactobacilli-adapted Iscoves Medium (SLIM) which leads to robust L. iners growth, a vaginally adapted version of SLIM (SLIM-V) and a chemically defined medium (SLIM-CD). SLIM and SLIM-V lead to dramatically improved L. iners growth compared to previously published formulations and support growth of other vaginal bacteria, including L. crispatus, L. jensenii, L. gasseri and G. vaginalis. SLIM-CD leads to slower growth but could prove useful for characterizing L. iners nutrient requirements or metabolite production. A modified version of SLIM-V supports growth of human cervical epithelial cells and provides a base for future co-culture work. Here, we present the formulations of SLIM, SLIM-V and SLIM-CD, and compare the growth of bacterial strains and human cells in the media.

microbiology↗

bioRxiv2023

GRAS1 non-coding RNA protects against DNA damage and cell death by binding NKAP

Non-coding RNA (ncRNA) gene products are involved in diverse biological processes including splicing, epigenetic regulation, gene expression, proliferation, and metabolism. The biological mechanisms by which ncRNAs contribute to cell survival remain poorly understood. We found that the Growth Regulator Antisense 1 (GRAS1) long non-coding RNA (lncRNA) transcript promotes growth in multiple human cell types by protecting against DNA damage. Knockdown of GRAS1 induced DNA damage and cell death, along with significant expression changes in DNA damage response, intrinsic apoptotic signaling, and cellular response to environmental stimulus genes. Extensive DNA damage occurred after GRAS1 knockdown, with numerous double strand breaks occurring in each cell. The number of cells undergoing apoptosis and with fragmented nuclei increased significantly after GRAS1 knockdown. We used RNA antisense purification and mass spectrometry (RAP-MS) to identify the NF-{kappa}B activating protein (NKAP) as a direct protein interaction partner of GRAS1 lncRNA. NKAP protein was degraded after GRAS1 knockdown, in a proteasome-dependent manner. Overexpression of GRAS1 or NKAP mitigated the DNA damage effects of GRAS1 knockdown. In summary, GRAS1 and NKAP directly interact to protect against DNA damage and cell death in multiple human cell lines.

molecular biology↗

bioRxiv2020

Integrative genomics identifies lncRNA regulatory networks across 1,044 pediatric leukemias and solid tumors

Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curate RNA sequencing data for 1,044 pediatric leukemia and solid tumors and integrate paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 exhibiting histotype-specific expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multi-dimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell-type specific transcription factors further implicated distinct histotype-specific and developmental lncRNAs. We integrated our analyses to prioritize lncRNAs for experimental validation and showed that silencing of TBX2-AS1, our top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming our computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.

cancer biology↗

bioRxiv2017

Adsorption and conformation of lysozyme and α-lactalbumin at water-octane interface

As they contain both hydrophobic and hydrophilic amino acids proteins will readily adsorb onto interfaces between water and hydrophobic fluids such as oil. This adsorption normally causes changes in protein structure, which can result in a loss of protein function and irreversible adsorption, leading to the formation of protein interfacial films. While this can be advantageous in some applications (e.g. food technology) in most cases it limits our ability to exploit protein functionality at interfaces. To understand and control protein interfacial adsorption and function it is necessary to understand the microscopic conformation of proteins at liquid interfaces. In this paper molecular dynamics simulations are used to investigate the adsorption and conformation of two similar proteins, lysozyme and -lactalbumin, at a water-octane interface. While they both adsorb onto the interface -lactalbumin does so in a specific orientation, mediated by two amphipathic helices, while lysozyme adsorbs in a non-specific manner. Using replica exchange simulations both proteins are found to possess a number of distinct interfacial conformations, with compact states similar to the solution conformation being most common for both proteins. Decomposing the different contributions to the protein energy at oil-water interfaces, suggests that conformational change for -lactalbumin, unlike lysozyme, is driven by favourable protein-oil interactions. Revealing these differences between the factors that govern conformational change at interfaces in otherwise similar proteins can give insight into the control of protein interfacial adsorption, aggregation, and function.

biophysics↗