Biology subjects

Abdallah, K.

Publications and source records attributed to Abdallah, K..

7 recordsLinked to original sources

bioRxiv2026

Sex differences in epigenetic mechanisms of chronic pain-induced depression

Chronic pain is a major risk factor for depression, yet the molecular mechanisms underlying this comorbidity remain poorly understood, particularly in women. To address this gap, we systematically investigated sex differences in the epigenomic adaptations associated with chronic pain-induced depressive-like behaviors. Neuropathic pain was induced in the mouse using the sciatic nerve cuff model, and molecular analyses were performed in the anterior cingulate cortex (ACC), a key brain region implicated in both pain and affective processing. We profiled genome-wide DNA methylation, three histone modifications (H3K27ac, H3K4me1, and H3K27me3), and gene expression using EM-seq, Cut&Tag sequencing, and RNA-seq, respectively. Differential analyses were conducted for each molecular layer and integrated through gene co-expression network analysis. We found that chronic pain induced extensive remodeling of DNA methylation and histone modification landscapes in both sexes. Strikingly, these changes occurred at largely distinct genomic loci in males and females, revealing pronounced sex-specific epigenetic responses. Despite this divergence, the affected regions displayed similar regulatory organization, including enrichment at shared genic features, transcription factor binding sites, and chromatin profiles. Importantly, these adaptations converged on partly overlapping genes, biological pathways, and co-expression modules across sexes. The most affected gene modules were predominantly associated with synapse-related processes, consistent with previous knowledge, and were closely connected to modules enriched for epigenetic regulatory functions. Together, these findings indicate that chronic pain engages sex-specific epigenetic mechanisms that ultimately converge on common functional outcomes. Such convergence highlights the potential value of targeting sex-specific epigenetic substrates in future therapeutic strategies.

neuroscience↗

bioRxiv2025

Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation

Despite recent advances in technology to map RNA chemical modifications transcriptome-wide, the distribution of N{superscript 1}-methyladenosine (m{superscript 1}A) in mRNA remains contested, hindering a clear understanding of its function. Additionally, the enzyme(s) that installs the majority of reported mRNA m1A sites has yet to be identified. In this study, we characterized TRMT61B, an m1A methyltransferase known to methylate mitochondrial RNAs, but whose sequence preferences have been underexplored. By integrating cellular overexpression of TRMT61B and in vitro methylation of a synthetic pool of diverse human RNA sequences, we identified a preference for a YMRA consensus motif in single stranded RNA regions. In these experiments, TRMT61B methylated thousands of novel human mRNA sites, revealing activity on cytosolic mRNAs. We used these novel m1A-modifiable sequences to test the effects of m1A on translation of luciferase reporters and on ribosome recruitment to modified transcripts in the pool. We found that m1A addition can significantly affect translation and ribosome recruitment, but that these effects are vary by transcript. Taken together, our results can inform future studies of TRMT61B and mRNA, and emphasize that studies of m1A regulation of mRNA must be carried out and interpreted in a highly context-aware manner.

biochemistry↗

bioRxiv2025

Repeated restraint stress-induced increase in post-surgical somatosensory hypersensitivity and affective responding is mediated by β-adrenergic receptor activation and spinal NLRP3-IL1β signalling in male rats

Pre-surgical stress is a well-recognised risk factor for persistent post-surgical pain, and while the precise underlying neurobiological mechanisms remain unknown, neuro-immune interactions are believed to play a pivotal role. Here, we investigated the effect of repeated restraint stress (RRS) on post-surgical somatosensory hypersensitivity and affective responding in male rats and examined underlying mechanisms mediating these effects. We showed that RRS induced behavioural despair in the forced swim test, reduced body weight gain and elevated faecal corticosterone levels in male Sprague-Dawley rats. Following paw-incision surgery, animals pre-exposed to RRS exhibited exacerbated mechanical and heat hypersensitivity, pain-related aversion, and anxiety-like behaviour compared to non-stress counterparts. RNAseq analysis revealed alterations in glial and neuro-immune pathways in the dorsal horn of the spinal cord in the RRS + paw incision group compared to paw incision alone, data further confirmed by increased microglial activity and inflammatory gene expression (iba1, itgam, il-1{beta} and nlrp3). Intrathecal administration of IL-1Ra or MCC950 (an NLRP3 inhibitor) attenuated the RRS-induced increase in pain-related aversion and mechanical hypersensitivity post-surgery. Chronic administration of RU486, a glucocorticoid receptor antagonist, prevented RRS-induced despair-like behaviour but did not alter the effects of RRS on pain-related aversion or mechanical hypersensitivity post-surgery. In contrast, chronic administration of propranolol, a {beta}-adrenergic receptor antagonist and sympathetic nervous system inhibitor, not only prevented the RRS-induced despair-like behaviour but also attenuated exacerbation of mechanical hypersensitivity, pain-related aversion, and anxiety-like behaviour post-surgery. These findings suggest that RRS exacerbates and prolongs post-surgical somatosensory and affective pain responding via {beta}-adrenergic receptor activation and increased spinal microglial NLRP3-IL1{beta} signalling. These data provide further insight into the mechanisms by which chronic stress and mood disorders exacerbate and prolong post-surgical pain.

neuroscience↗

bioRxiv2024

An atypical E3 ligase safeguards the ribosome during nutrient stress

Metabolic stress must be effectively mitigated for the survival of cells and organisms. Ribosomes have emerged as signaling hubs that sense metabolic perturbations and coordinate responses that either restore homeostasis or trigger cell death. As yet, the mechanisms governing these cell fate decisions are not well understood. Here, we report an unexpected role for the atypical E3 ligase HOIL-1 in safeguarding the ribosome. We find HOIL-1 mutations associated with cardiomyopathy broadly sensitize cells to nutrient and translational stress. These signals converge on the ribotoxic stress sentinel ZAK. Mechanistically, mutant HOIL-1 excludes a ribosome quality control E3 ligase from its functional complex and remodels the ribosome ubiquitin landscape. This quality control failure renders glucose starvation ribotoxic, precipitating a ZAK-ATF4-xCT-driven noncanonical cell death. We further show HOIL-1 loss exacerbates cardiac dysfunction under pressure overload. These data reveal an unrecognized ribosome signaling axis and a molecular circuit controlling cell fate during nutrient stress.

cell biology↗

bioRxiv2021

NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database

RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.

biophysics↗

bioRxiv2020

Sex-specific retinal anomalies induced by chronic social stress in mice

Major depressive disorder (MDD) is one of the most common consequences of chronic stress. Still, there is currently no reliable biomarker to detect individuals at risk to develop MDD. Recently, the retina emerged as an effective way to approach the brain and investigate psychiatric disorders with the use of the electroretinogram (ERG). In this study, cones and rods ERGs were performed in male and female mice before and after chronic social defeat stress (CSDS). Mice were then divided as susceptible or resilient to stress. Significant results were only observed in rods ERGs. In males, susceptible mice showed prolonged a-wave implicit times at baseline that were shortened after CSDS. The a-wave was also decreased in both susceptible and resilient male mice after CSDS. In females, rod a-waves were shorter in susceptible than in control mice after CSDS resulting from the latter demonstrating delayed a-waves. Baseline ERGs were able to predict - to some extent - the expression of susceptibility and resilience before stress exposition in male and female mice. Overall, our findings suggest that retinal activity is a presumptive biomarker of stress response and that the ERG could potentially serve as a predicting tool of the stress response in mice.

neuroscience↗

bioRxiv2016

A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients

BackgroundDocetaxel has a demonstrated survival benefit for metastatic castration-resistant prostate cancer (mCRPC). However, 10-20% of patients discontinue docetaxel prematurely because of toxicity-induced adverse events, and managing risk factors for toxicity remains an ongoing challenge for health care providers and patients. Prospective identification of high-risk patients for early discontinuation has the potential to assist clinical decision-making and can improve the design of more efficient clinical trials. In partnership with Project Data Sphere (PDS), a non-profit initiative facilitating clinical trial data-sharing, we designed an open-data, crowdsourced DREAM (Dialogue for Reverse Engineering Assessments and Methods) Challenge for developing models to predict early discontinuation of docetaxel\n\nMethodsData from the comparator arms of four phase III clinical trials in first-line mCRPC were obtained from PDS, including 476 patients treated with docetaxel and prednisone from the ASCENT2 trial, 598 patients treated with docetaxel, prednisone/prednisolone, and placebo in the VENICE trial, 526 patients treated with docetaxel, prednisone, and placebo in the MAINSAIL trial, and 528 patients treated with docetaxel and placebo in the ENTHUSE 33 trial. Early discontinuation was defined as treatment stoppage within three months due to adverse treatment effects. Over 150 clinical features including laboratory values, medical history, lesion measures, prior treatment, and demographic variables were curated and made freely available for model building for all four trials. The ASCENT2, VENICE, and MAINSAIL trial data sets formed the training set that also included patient discontinuation status. The ENTHUSE 33 trial, with patient discontinuation status hidden, was used as an independent validation set to evaluate model performance. Prediction performance was assessed using area under the precision-recall curve (AUPRC) and the Bayes factor was used to compare the performance between prediction models.\n\nResultsThe frequency of early discontinuation was similar between training (ASCENT2, VENICE, and MAINSAIL) and validation (ENTHUSE 33) sets, 12.3% versus 10.4% of docetaxel-treated patients, respectively. In total, 34 independent teams submitted predictions from 61 different models. AUPRC ranged from 0.088 to 0.178 across submissions with a random model performance of 0.104. Seven models with comparable AUPRC scores (Bayes factor [≤]; 3) were observed to outperform all other models. A post-challenge analysis of risk predictions generated by these seven models revealed three distinct patient subgroups: patients consistently predicted to be at high-risk or low-risk for early discontinuation and those with discordant risk predictions. Early discontinuation events were two-times higher in the high-versus low-risk subgroup and baseline clinical features such as presence/absence of metastatic liver lesions, and prior treatment with analgesics and ACE inhibitors exhibited statistically significant differences between the high- and low-risk subgroups (adjusted P < 0.05). An ensemble-based model constructed from a post-Challenge community collaboration resulted in the best overall prediction performance (AUPRC = 0.230) and represented a marked improvement over any individual Challenge submission. A\n\nFindingsOur results demonstrate that routinely collected clinical features can be used to prospectively inform clinicians of mCRPC patients risk to discontinue docetaxel treatment early due to adverse events and to the best of our knowledge is the first to establish performance benchmarks in this area. This work also underscores the \"wisdom of crowds\" approach by demonstrating that improved prediction of patient outcomes is obtainable by combining methods across an extended community. These findings were made possible because data from separate trials were made publicly available and centrally compiled through PDS.

bioinformatics↗