Biology subjects

Cote, A.

Publications and source records attributed to Cote, A..

12 recordsLinked to original sources

bioRxiv2025

Comprehensively Testing the Function of Missense Variation in the STK11 Tumour Suppressor

The tumor suppressor gene STK11 encoding Serine/Threonine Kinase 11 (STK11) is associated with Peutz-Jeghers Syndrome (PJS), a heritable gastrointestinal disease that increases lifetime cancer risk, and with somatic variation that contributes to [~]30% of lung and 20% of cervical cancers. Although identifying pathogenic variants is clinically actionable, over 94% of STK11 missense variants that have been observed clinically lack a definitive classification. We therefore measured the impact of STK11 variants at scale in a mammalian cell-based assay, scoring 6,026 (73% of all possible) amino acid substitutions across the full-length gene. Functional scores--which were consistent with biochemical properties, smaller-scale assays, and pathogenicity annotations--identified a subset of PJS patients with germline STK11 variants diagnosed later in life, as well as somatic STK11 variants found in cancer patients that had comparable overall survival estimates to wild-type STK11. Our scores provided new evidence for 350 annotated VUS STK11 missense variants and [~]80% of missense variants that have not yet been reported clinically, but we might expect to observe in the future. Thus, our effect map provides a proactive resource for gaining sequence-structure-function insights and evidence for actionable interpretation of clinical missense variants.

cancer biology↗

bioRxiv2025

Alterations to cellular metabolism are linked to multiple natural parasite infections across populations of a freshwater fish

Exposure to environmental stressors can induce physiological responses in organisms, which can lead to population-level differences in physiological traits. However, the mechanisms underlying these responses both within individuals and among populations are often unknown. Parasite infections, in particular, are important biotic stressors that can induce a range of effects in hosts, including altered whole-organism metabolism. However, few studies have explored sub-cellular alterations to metabolic performance across both an individual infection gradient and population-level differences in infection prevalence. We compared mitochondrial enzyme activities across five distinct populations of pumpkinseed sunfish (Lepomis gibbosus) differing in the prevalence of cestode and trematode parasites. Overall, we found that enzymes from the OXPHOS pathway (cytochrome c oxidase, NADH dehydrogenase and coenzyme Q : cytochrome c oxidoreductase), the anaerobic pathway (lactate dehydrogenase), the TCA cycle (citrate synthase) and lipid metabolism (carnitine palmitoyl transferase) were positively correlated with parasite density with trends depending on the organ, parasite species and host population studied. Our results suggest complex and nuanced relationships among infections and host physiological performance and provide strong evidence of parasite-induced alterations to mitochondrial metabolism which may explain previously reported whole-organism responses to infections.

ecology↗

bioRxiv2024

Decoding the transcriptomic signatures of psychological trauma in human cortex and amygdala

Psychological trauma has profound effects on brain function and precipitates psychiatric disorders in vulnerable individuals, however, the molecular mechanisms linking trauma with psychiatric risk remain incompletely understood. Using RNA-seq data postmortem brain tissue of a cohort of 304 donors (N=136 with trauma exposure), we investigated transcriptional signatures of trauma exposures in two cortical regions (dorsolateral prefrontal cortex, and dorsal anterior cingulate cortex) and two amygdala regions (medial amygdala and basolateral amygdala) associated with stress processing and regulation. We focused on dissecting heterogeneity of traumatic experiences in these transcriptional signatures by investigating exposure to several trauma types (childhood, adulthood, complex, single acute, combat, and interpersonal traumas) and interactions with sex. Overall, amygdala regions were more vulnerable to childhood traumas, whereas cortical regions were more vulnerable to adulthood trauma (regardless of childhood experience). Using cell-type-specific expression imputation, we identified a strong transcriptional response of medial amygdala excitatory neurons to childhood trauma, which coincided with dysregulation observed in a human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons exposed to hydrocortisone. We resolved multiscale coexpression networks for each brain region and identified modules enriched in trauma signatures and whose connectivity was altered with trauma. Trauma-associated coexpression modules provide insight into coordinated functional dysregulation with different traumas and point to potential gene targets for further dissection. Together, these data provide a characterization of the long-lasting human encoding of traumatic experiences in corticolimbic regions of human brain.

neuroscience↗

bioRxiv2024

The importance of visual and chemical cues in infection detection and avoidance in a freshwater fish

The characteristics of infected animals, including their smell, appearance, behaviour or sound, can greatly differ from those of uninfected conspecifics. These differences can serve as cues to recognize and avoid infected individuals to minimize the risk of infection. Avoidance of infected conspecifics is a risk-sensitive behaviour that can be influenced by various factors such as sensory cues and environmental parasite load, which both remain poorly understood in fish. We investigated the ability of two populations of wild caught pumpkinseed sunfish (Lepomis gibbosus) to distinguish between conspecifics infected with parasitic worms versus uninfected individuals in two-choice experiments using visual and chemical cues separately. One population was from a lake without parasites (parasite naive) whereas the other population originated from a lake with a high prevalence of trematode and cestode worms (parasite experienced). Both populations preferred to be with conspecifics, regardless of their infection level, over being alone when given visual cues but avoided conspecifics and remained alone when given chemical cues, suggesting that visual and chemical cues are not redundant. Neither population showed any preference between infected and uninfected conspecifics when given visual cues. However, in the presence of chemical cues, there was a great interindividual variation: some fish preferred uninfected conspecifics while others preferred infected ones. On average, naive fish avoided infected conspecifics whereas experienced fish did not show any preferences, suggesting that fish from lakes with high prevalence of infection habituate to infection cues. We suggest that pumpkinseeds use chemical rather than visual cues to discriminate between infected and uninfected conspecifics and make a shoaling decision. Our study highlights the importance of considering different sensory cues as well as parasite load when studying avoidance and shoaling behaviours, especially in a time of modifying sensory landscape and parasites abundance of freshwater ecosystems through global changes.

animal behavior and cognition↗

bioRxiv2023

Common genetic variation impacts molecular stress response in the brain

To explain why individuals exposed to identical stressors experience divergent clinical outcomes, we determine how molecular encoding of stress modifies genetic risk for brain disorders. Analysis of post-mortem brain (n=304) revealed 8557 stress-interactive expression quantitative trait loci (eQTLs) that dysregulate expression of 915 eGenes in response to stress, and lie in stress-related transcription factor binding sites. Response to stress is robust across experimental paradigms: up to 50% of stress-interactive eGenes validate in glucocorticoid treated hiPSC-derived neurons (n=39 donors). Stress-interactive eGenes show brain region- and cell type-specificity, and, in post-mortem brain, implicate glial and endothelial mechanisms. Stress dysregulates long-term expression of disorder risk genes in a genotype-dependent manner; stress-interactive transcriptomic imputation uncovered 139 novel genes conferring brain disorder risk only in the context of traumatic stress. Molecular stress-encoding explains individualized responses to traumatic stress; incorporating trauma into genomic studies of brain disorders is likely to improve diagnosis, prognosis, and drug discovery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/573459v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1e07fa9org.highwire.dtl.DTLVardef@1dd530forg.highwire.dtl.DTLVardef@17822a5org.highwire.dtl.DTLVardef@2a889f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Thermal tolerance and survival are modulated by a natural gradient of infection in differentially acclimated hosts

Wild ectotherms are exposed to multiple stressors, including parasites, which can affect their responses to environmental change. Simultaneously, unprecedented warm temperatures are being recorded worldwide, increasing both the average and maximum temperatures experienced in nature. Understanding how ectotherms, such as fishes, will react to the combined stress of parasites and higher average temperatures can help predict the impact of extreme events such as heat waves on populations. The critical thermal method (CTM), which assesses upper (CTmax) and lower (CTmin) thermal tolerance, is often used in acclimated ectotherms to help predict their tolerance to various temperature scenarios. Yet, few studies have characterized the response of naturally infected fish to extreme temperature events or how acute thermal stress affects subsequent survival. We acclimated naturally infected pumpkinseed sunfish (Lepomis gibbosus), to four ecologically relevant temperatures (10, 15, 20 and 25{degrees}C) and one future warming scenario (30{degrees}C) for three weeks, before measuring CTmax and CTmin. We also assessed individual survival the week following CTmax. Interestingly, trematode parasites causing black spot disease were negatively related to CTmax, suggesting that heavily infected fish are less tolerant to acute warming. Moreover, fish infected with yellow grub parasites showed decreased survival in the days following CTmax implying that the infection load has negative survival consequences on sunfish during extreme warming events. Our findings indicate that parasite infection and high prolonged average temperatures can affect fish thermal tolerance and survival, emphasizing the need to better understand the concomitant effects of stressors on health outcomes in wild populations. Summary statementThis study shows that parasites influence thermal tolerance and survival of fish, suggesting that such stressors are important to increase the ecological relevance of thermal tolerance studies of wild animals.

ecology↗

bioRxiv2022

satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

BackgroundThe impact of thousands of individual genetic variants on molecular phenotypes for disease-relevant genes remains unknown. Multiplexed assays for variant effect (MAVEs) are highly scalable methods to annotate the relevant variants. However, current software methods for analyzing MAVEs lack standardized annotation, can require cumbersome configuration, and do not easily scale to large target regions. ResultsHere, we present satmut_utils as a flexible solution for 1) simulation of saturation mutagenesis data; and 2) quantification of variants across four orders of magnitude from multiplexed assay data. Improvements of satmut_utils over existing solutions include support for multiple experimental strategies, unique molecular identifier-based consensus deduplication, and machine learning-based error correction. We developed a rigorous simulation workflow to validate the performance of satmut_utils and carried out the first benchmarking of existing software for variant calling. Finally, we used satmut_utils to determine the mRNA abundance of thousands of coding variants in cystathionine beta-synthase (CBS) by two library preparation methods. We identified an association between variants near chemical cofactor binding sites and decreased mRNA abundance. We also found a correlation between codon optimality and the magnitude of variant effects, emphasizing the potential of single-nucleotide variants to alter mRNA abundance. Conclusionssatmut_utils enables high-performance analysis of saturation mutagenesis data, achieves unprecedented specificity through novel error correction approaches, and reveals the capability of single-codon variants to alter mRNA abundance in native coding sequences.

genomics↗

bioRxiv2021

Well-Lit: A programmable and customizable assistant for manual multi-well plate pipetting

A very large number of biology and biochemistry laboratory protocols require transferring liquid aliquots from individual containers into individual wells of a multi-well plate, from plates to individual containers, or from one plate to another. Doing this by hand without errors, such as skipping wells, placing two samples in the same well, or swapping sample locations, especially when using plates with 96 wells or more, is difficult and requires enormous operator focus and/or a tedious manual error checking system. We present here a device built to facilitate error-free pipetting of samples from individual barcoded tubes to a multi-well plate or between multi-well plates (both 96 and 384 wells are supported). The device is programmable, modular and easily customizable to accommodate plates with different form-factors, and different protocols. The main components are only a 12.3" touch screen, a small form-factor PC, and a barcode scanner, combined with custom-made parts can be easily fabricated with a laser cutter and a hobby-grade 3D printer. The total cost is between approximately US$550 and US$600, depending on the configuration. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@8554f4org.highwire.dtl.DTLVardef@18c8878org.highwire.dtl.DTLVardef@153b050org.highwire.dtl.DTLVardef@15c7de6org.highwire.dtl.DTLVardef@14daeb7_HPS_FORMAT_FIGEXP M_TBL C_TBL

bioengineering↗

bioRxiv2021

CTCF blocks anti-sense transcription initiation at divergent gene promoters

Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is largely unknown. Here by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters, the great majority of which bear proximal CTCF binding sites. Genome editing, chromatin conformation studies, and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its chromatin architectural function. Primary transcript RNA FISH revealed co-bursting of sense and anti-sense transcripts is disfavored, suggesting CTCF-regulated competition for transcription initiation. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.

molecular biology↗

bioRxiv2020

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-{beta}), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined accessibility response was the sum of the accessibility responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.

systems biology↗

bioRxiv2017

Single-molecule fluorescent amplification of RNA using clampFISH probes

Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of RNA that combines the specificity of oligonucleotides with bioorthogonal click chemistry in order to achieve high specificity and extremely high-gain (>400x) signal amplification. We show that clampFISH signal enables detection with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH works in tissue samples.

bioengineering↗

bioRxiv2017

Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics

Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double mutant strains, does not scale readily to multi-condition studies. Here we describe Barcode Fusion Genetics to map Genetic Interactions (BFG-GI), by which double mutant strains generated via en masse party mating can also be monitored en masse for growth and genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to a decrease in the activation or activity of the checkpoint protein kinase Rad53.

systems biology↗