Biology subjects

Currie, J.

Publications and source records attributed to Currie, J..

8 recordsLinked to original sources

bioRxiv2026

Spatiotemporal Heterogeneity of HPV Integration Architectures Drive Oncogenic Features of Oropharyngeal Cancer

Viral integration is common in human papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC), but its structural and clinical significance remains unclear. We integrated targeted capture sequencing of 197 HPV+ OPSCCs with long-read nanopore sequencing of 17 tumors and models to characterize HPV-host rearrangements. We developed a novel quantitative informatics framework that classifies integration structures as Type1 (simple, single/low-copy) or Type2 (clustered, high-copy, rearranged). HPV integration occurred in 83% of tumors, with recurrent hotspots including TP63, MYC, CD274, TRAF2, and KMT2C. Type2 events were enriched for HPV E2 disruption, focal human amplifications, preferential transcription, and noncanonical HPV-host RNA fusion isoforms. Type2 tumors showed increased HPV oncogene expression and activation of MYC, NF-{kappa}B/TNF, PI3K-AKT-mTOR, Hippo/YAP-TAZ, and epithelial stemness programs. Multi-region and longitudinal analyses revealed intratumoral heterogeneity and clonal selection of Type2 architectures during progression, supporting integration structure as a potential marker of aggressive behavior and risk stratification.

bioinformatics↗

bioRxiv2025

PLD1-Dependent Regulation of Synaptic Integrity: Implications for Cognitive Resilience and Alzheimer's Disease Pathogenesis

Dysregulation of Phospholipase D1 (PLD1) has been implicated in the progression of neurodegenerative diseases, including Alzheimers Disease (AD). This study investigated PLD1 signaling in synaptic integrity and cognition during aging and in a late-onset AD mouse model, hypothesizing differential effects of PLD1 modulation on synaptic vulnerability. AAV2-mediated gene transfer was employed to overexpress (PLD1 OXP) or attenuate (PLD1 ATT) PLD1 in aged wild-type (WT) and 3xTg-AD mice. To validate these constructs, differentiated PC12 cells were utilized. Within these cells, a model of post-mitotic neurons, PLD1 OXP exhibited a notable reduction in both the average neurite length and the percentage of neurite-bearing cells. This suggests that elevated PLD1 activity exerts a significant influence on neurite outgrowth. Conversely, PLD1 ATT did not inhibit neurite formation, indicating it is not detrimental at the cellular level. These cellular findings paralleled in vivo observations - electrophysiological studies revealed PLD1 OXP impaired long-term potentiation (LTP) and synaptic transmission, particularly in aged WT mice, whereas PLD1 ATT improved synaptic function in 3xTg-AD mice. Behaviorally, PLD1 ATT enhanced spatial working memory and reduced anxiety-like behavior, notably in 3xTg-AD mice. These results highlight that tight PLD1 regulation is vital for maintaining synaptic integrity and cognitive resilience. Thus, PLD1 attenuation may serve as an important complement to immunotherapeutic approaches by strengthening synaptic resilience in neurodysfunctional states, including AD and related dementia (ADRD).

neuroscience↗

bioRxiv2025

Navigating methodological decisions: Balancing rigor and data volume of the Canadian Living Planet Index

The Living Planet Index -- a biodiversity indicator that assesses the relative change of aggregate vertebrate abundance data -- is an indicator used in global and national biodiversity monitoring frameworks. In Canada, the LPI has been modified (C-LPI) -- adopting differing methodological choices relative to the global LPI. However, there is no clear consensus on the most appropriate analytical methods, particularly as they pertain to the treatment of zeros, confidence intervals and uncertainty, time series length and number of data points required, modelling of short time series, removal of outliers, weighting species, and the impact of baseline year selection. Our analysis transparently explores multiple methodological options and the consequent C-LPI output for each of these decision points. Our research does not evaluate the superiority of a single approach but rather provides transparency and accountability in C-LPI reporting. We hope that this will further strengthen the utility of the C-LPI and provide decision makers with the necessary information to appropriately interpret patterns, evaluate progress towards biodiversity targets, and inform conservation action.

ecology↗

bioRxiv2025

Deuterium labeling enables proteome wide turnover kinetics analysis in cell culture

The half-life of proteins is tightly regulated and underlies many cellular processes. It remains unclear the extent to which proteins are dynamically synthesized and degraded in different cell types and cell states. We introduce an improved D2O labeling workflow and apply it to examine the landscape of protein turnover in pluripotent and differentiating human induced pluripotent stem cells (hiPSC). The majority of hiPSC proteins show minimal turnover beyond cell doubling rates, but we also identify over 100 new fast-turnover proteins not previously described as short-lived. These include proteins that function in cell division and cell cycle checkpoints, that are enriched in APC/C and SPOP degrons, and that are depleted upon pluripotency exit. Differentiation rapidly shifts the set of fast-turnover proteins toward including RNA binding and splicing proteins. The ability to identify fast-turnover proteins in different cell cultures also facilitates secretome analysis, as exemplified by studies of hiPSC-derived cardiac myocytes and primary human cardiac fibroblasts. The presented workflow is broadly applicable to protein turnover studies in diverse primary, pluripotent, and transformed cells.

biochemistry↗

bioRxiv2024

Synaptic gene expression is coordinated across development by conserved chromatin regulators

Synapses are the primary sites of communication in the nervous system. Synapse formation requires the simultaneous expression of hundreds of proteins across cells. Through genomic and functional studies in Drosophila, we investigated the regulatory mechanisms underlying the spatiotemporal coordination of synaptic gene expression during neurodevelopment. We find that chromatin opening is coordinated across hundreds of synaptic genes immediately preceding transcription, whereas repression of these genes outside developmental periods of synaptogenesis is regulated by distinct mechanisms. We identify the conserved DEAF1 transcription factor (TF) as a direct repressor of synaptic genes. Disruption of DEAF1 or pioneer TF CLAMP, which promotes DEAF1 binding, increases synaptic gene expression across neuronal subtypes, leading to excess synapse formation. DEAF1, which is linked to syndromic intellectual disability, is also sufficient to block synaptogenesis. These findings reveal the importance of coordinated synaptic gene repression in sculpting neuronal connectivity and broaden our understanding of gene regulation in neurodevelopment.

neuroscience↗

bioRxiv2024

Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection

The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical approaches to derive turnover rates from the isotopomer patterns of deuterium labeled peptides continue to be a subject of research. Here we describe a method, which comprises a reverse lookup of numerically approximated peptide isotope envelopes, coupled to the selection of optimal isotopomer pairs based on peptide sequence, to calculate the molar fraction of new peptide synthesis in heavy water labeling mass spectrometry experiments. We validated this approach using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes. We then re-analyzed 17 proteome-wide turnover experiments from four mouse organs, and showed that the method increases the coverage of well-fitted peptides in protein turnover experiments by 25-82%. The method is implemented in the Riana software tool for protein turnover analysis, and may avail ongoing efforts to study the synthesis and degradation kinetics of proteins in animals on a proteome-wide scale. Whats newWe describe a reverse lookup method to calculate the molar fraction of new synthesis from numerically approximated peptide isotopomer profiles in heavy water labeling mass spectrometry experiments. Using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes at various proportions, we show that this method provides a straightforward way to calculate the proportion of new proteins in a protein pool from arbitrarily chosen isotopomer ratios. We next analyzed which of the isotopomer pairs within the peptide isotope envelope yielded isotopomer time courses that fit most closely to kinetic models, and found that the identity of the isotopomer pair depends partially on the number of deuterium accessible labeling sites of the peptide. We next derived a strategy to automatically select the isotopomer pairs to calculate turnover rates based on peptide sequence, and showed that this increases the coverage of existing proteome-wide turnover experiments in multiple data sets of the mouse heart, liver, kidney, and skeletal muscle by up to 25-82%.

biochemistry↗

bioRxiv2023

Simultaneous proteome localization and turnover analysis reveals spatiotemporal dynamics of unfolded protein responses

The functions of proteins depend on their spatial and temporal distributions, which are not directly measured by static protein abundance. Under endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) pathway remediates proteostasis in part by altering the turnover kinetics and spatial distribution of proteins. A global view of these spatiotemporal changes has yet to emerge and it is unknown how they affect different cellular compartments and pathways. Here we describe a mass spectrometry-based proteomics strategy and data analysis pipeline, termed Simultaneous Proteome Localization and Turnover (SPLAT), to measure concurrently the changes in protein turnover and subcellular distribution in the same experiment. Investigating two common UPR models of thapsigargin and tunicamycin challenge in human AC16 cells, we find that the changes in protein turnover kinetics during UPR varies across subcellular localizations, with overall slowdown but an acceleration in endoplasmic reticulum and Golgi proteins involved in stress response. In parallel, the spatial proteomics component of the experiment revealed an externalization of amino acid transporters and ion channels under UPR, as well as the migration of RNA-binding proteins toward an endosome co-sedimenting compartment. The SPLAT experimental design classifies heavy and light SILAC labeled proteins separately, allowing the observation of differential localization of new and old protein pools and capturing a partition of newly synthesized EGFR and ITGAV to the ER under stress that suggests protein trafficking disruptions. Finally, application of SPLAT toward human induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) exposed to the cancer drug carfilzomib, identified a selective disruption of proteostasis in sarcomeric proteins as a potential mechanism of carfilzomib-mediated cardiotoxicity. Taken together, this study provides a global view into the spatiotemporal dynamics of human cardiac cells and demonstrates a method for inferring the coordinations between spatial and temporal proteome regulations in stress and drug response.

cell biology↗

bioRxiv2022

Past, present, and future of the Living Planet Index

As we enter the next phase of international policy commitments to halt biodiversity loss (e.g. Post-2020 Biodiversity Framework), biodiversity indicators will play an important role forming the robust basis upon which targeted, and time sensitive conservation actions are developed. Population trend indicators are perhaps the most powerful tool in biodiversity monitoring due to their responsiveness to changes over short timescales and their ability to aggregate species trends from global down to at a sub-national or even local scale. We consider how the project behind the foremost population level indicator - the Living Planet Index - has evolved over the last 25 years, its value to the field of biodiversity monitoring, and how its components have portrayed a compelling account of the changing status of global biodiversity through its application at policy, research and practice levels. We explore ways the project can develop to enhance our understanding of the state of biodiversity and share lessons learned to inform indicator development and mobilise action. O_TEXTBOXBox 1. The Living Planet Index Project The Living Planet Index project (the index, methodology, and database) and its secondary outputs (methods papers and R code, database and website, global index, and subset indices) have had wide-ranging applications within the fields of biodiversity monitoring and research, as well as across policy, education, and outreach. The Living Planet Index (LPI) is a biodiversity indicator which tracks trends in the relative abundance of wild vertebrate populations (where population is defined as to a single species in a defined location rather than the biological definition). Relative abundance captures how populations are changing over time on average in comparison to a reference point, or "baseline" (the LPI uses 1970). It is often described as analogous to a stock market index for species. The index is comprised of thousands of population time-series for vertebrate species from locations around the world; the trends from these populations are averaged to produce terrestrial, freshwater, and marine indices, which are further aggregated to a global LPI. The latest global LPI shows a decline of 68% between 1970 and 2016 globally 1. This is an average trend based on time-series data from 20,811 populations of 4,392 species of mammals, birds, reptiles, amphibians, and fish. The LPI database (LPD) can include population data for any species for which time-series population data could be found, regardless of threat status, or whether they show increasing or declining trends. These population time-series are sourced from scientific papers, online databases, government, and expert led published reports. They can be searched and downloaded from the project website (www.livingplanetindex.org). More technical information is available on the LPI stats website (http://stats.livingplanetindex.org/). C_TEXTBOX

ecology↗