Biology subjects

Gadey, L.

Publications and source records attributed to Gadey, L..

4 recordsLinked to original sources

bioRxiv2026

Transcriptomics of cold stress and recovery reveal strongly tissue-specific responses

Cellular stress responses are often characterized as conserved, cell-autonomous processes. However, it remains unclear whether stress responses are coordinated uniformly across tissues within complex organisms, particularly during ecologically relevant conditions. We investigated tissue- and stage-specific transcriptional responses to cold stress in Drosophila melanogaster. Adults and larvae were independently exposed to a gradual cooling and recovery time series, and three adult tissues (gut, ovary, brain) and one larval tissue (gut) were sampled at baseline, at two time points that spanned the critical thermal minimum (before and during chill coma), and after recovery to rearing temperature. Transcriptomic analyses revealed strongly tissue- and stage-specific responses to cold stress, with limited overlap in differentially expressed genes or functional enrichment across tissues. These results indicate that the organismal response to thermal stress at the transcriptional level is not coordinated by a unified transcriptional program, but rather by largely distinct, tissue-specific regulatory processes.

bioinformatics↗

bioRxiv2025

Context-dependent regulatory variants in Alzheimer's disease

Noncoding genetic variants underlie many complex diseases, yet identifying and interpreting their functional impacts remains challenging. Late-onset Alzheimers disease (LOAD), a polygenic neurodegenerative disorder, exemplifies this challenge. The disease is strongly associated with noncoding variation, including common variants enriched in microglial enhancers and rare variants nominated at loci implicated in neurodevelopment and synaptic function. These variants may perturb regulatory sequences by disrupting transcription factor (TF) motifs or altering local regulatory sequence context, with potential consequences for gene expression and chromatin accessibility. However, assessing their impact is complicated by the context-dependent functions of regulatory sequences, underscoring the need to systematically examine variant effects across diverse tissues, cell types, and cellular states. Here, we combined in vitro and in vivo massively parallel reporter assays (MPRAs) with interpretable machine-learning models to systematically characterize common and rare variants across myeloid and neuron-enriched neural contexts. Parallel profiling of variants in four immune states in vitro and three mouse brain regions in vivo revealed that individual variants can differentially and even oppositely modulate reporter activity across cellular contexts, while a subset showed immune-state-dependent effects. Within the assayed candidate set, the relative effect sizes of common and rare variants reversed between contexts, with common variants showing larger effects in THP-1 macrophages and rare variants in brain tissue. Interpretable sequence-to-function models prioritized context-biased variants and generated motif-level hypotheses, including predicted transcription-factor motif disruption and subtler changes in local motif context. To probe endogenous consequences at a prioritized locus, we used CRISPR interference to perturb a rare-variant-containing enhancer at the SEC63-OSTM1 locus, revealing metabolic and biosynthetic transcriptional programs resembling those induced by SEC63 promoter perturbation, together with a stimulation-specific interferon response. These findings show that LOAD-associated noncoding variants exhibit context-dependent effects on reporter activity and predicted chromatin accessibility, and provide a framework for linking genetic association to regulatory activity, sequence grammar and endogenous transcriptional state.

genomics↗

bioRxiv2025

Combining Machine Learning and Multiplexed, In Situ Profiling to Engineer Cell Type and Behavioral Specificity

A promising strategy for the precise control of neural circuits is to use cis-regulatory enhancers to drive transgene expression in specific cells. However, enhancer discovery faces key challenges: low in vivo success rates, species-specific differences in activity, challenges with multiplexing adeno-associated viruses (AAVs), and the lack of spatial detail from single-cell sequencing. In order to accelerate enhancer discovery for the dorsal spinal cord--a region critical for pain and itch processing--we developed an end-to-end platform, ESCargoT (Engineered Specificity of Cargo Transcription), combining machine learning (ML)-guided enhancer prioritization, modular AAV assembly, and multiplexed, in situ screening. Using cross-species chromatin accessibility data, we trained ML models to predict enhancer activity in oligodendrocytes and in 15 dorsal horn neuronal subtypes. We first demonstrated that an initial enhancer, Excit-1, targeted excitatory dorsal horn neurons and drove reversal of mechanical allodynia in an inflammatory pain model. To enable parallel profiling of a 27-enhancer-AAV library delivered intraspinally in mice, we developed a Spatial Parallel Reporter Assay (SPRA) by integrating a novel Golden-Gate assembly pipeline with multiplexed, in situ screening. Regression adjustment for spatial confounding enabled specificity comparisons between enhancers, demonstrating the ability to screen enhancers targeting diverse cell types (oligodendrocytes, motoneurons, dorsal neuron subtypes) in one experiment. We then validated two candidates, targeting Exc-LMO3 and Exc-SKOR2 neurons, respectively. In a companion paper by Noh et al, our colleagues show that the functional specificity of the Exc-SKOR2-targeting enhancer, unlike Excit-1, is capable of blocking the sensation of chemical itch in mice. These enhancers were derived from the macaque genome but displayed functional sensitivity in mice. This platform enables spatially resolved, multiplexed in vivo enhancer profiling to accelerate discovery of cell-targeting tools and gene therapy development.

neuroscience↗

bioRxiv2023

Conserved cold tolerance of Rhagoletis species from different host fruits, elevations in Colorado, USA

Understanding and characterizing how insects tolerate low temperatures is important for predicting their overwintering survival and subsequent geographic spread. This study characterized the cold tolerance of two members of the Rhagoletis genus in Colorado, U.S.A. Pupae were collected from infested fruit in late summer and early fall. For the first time, we show that the rosehip fly Rhagoletis basiola is freeze-avoidant; overwintering pupae could supercool to temperatures as low as -26{degrees}C and survive. Interestingly, the temperature at which ice forms (supercooling point; SCP) did not vary between R. basiola at high (c. 2900 m above sea level) and lower (c. 1650 m a.s.l.) elevations. We also report the apple maggot Rhagoletis pomonella infesting an unusual host fruit, the Dolgo crabapple, in close proximity to infested hawthorn trees. R. pomonella infesting hawthorn fruits and crabapples had similar SCPs, and survived temperatures as low as -21{degrees}C. Pupae from both host fruits also survived prolonged exposure (2 weeks or more) to mild low temperatures (0 to -5{degrees}C). Further study into the mechanisms underlying the impressive and conserved cold tolerance of R. pomonella and R. basiola is an interesting avenue for future research.

zoology↗