Biology subjects

Nader, K.

Publications and source records attributed to Nader, K..

12 recordsLinked to original sources

bioRxiv2026

Improving reproducibility in pharmacogenomic screens through cross-study benchmarking

Drug-response measurements across pre-clinical pharmacogenomic studies remain poorly correlated, which limits biomarker discovery, precision oncology, and predictive modelling. The drivers of this inconsistency have been debated but not yet resolved. By integrating 15 pharmacogenomic studies encompassing 760 small-molecule compounds, 1,111 cell models, and 9.8 million dose-response measurements, we demonstrate that dose-response metric is the strongest driver of inconsistency, followed by experimental factors, such as treatment duration, plate format, and viability readout; in contrast, cell line molecular features contribute only minimally to reproducibility. Among drug classes, hormone therapies and PARP inhibitors show the highest concordance, whereas antimetabolites, topoisomerase inhibitors, and mitotic inhibitors exhibit substantial response variability across studies. To improve consistency, we developed a Drug Response Score (DRS), a proximity-weighted measure that emphasize pharmacologically informative concentrations near IC50, and we demonstrate in systematic benchmarking how DRS markedly improved cross-dataset concordance. Applications to patient-derived neuroblastoma organoids and leukemia patients primary cells demonstrate that DRS improves replicate-level consistency in patients drug-response profiles. To improve reproducible pharmacogenomic studies, we make openly available an integrated Drug Response Resource (iDRR, https://aittokallio.group/iDRR/), a standardized 15-dataset portal that supports robust biomarker discovery and cross-study benchmarking.

cancer biology↗

bioRxiv2026

Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing

Computational drug repurposing has largely been focused on rapid hypothesis generation, yet real-world applications span a far broader lifecycle, from drug candidate suggestion to designing experiments, analyzing assay data, and iteratively refining candidates. Here, we demonstrate that agentic AI can operate throughout this lifecycle. To this end, we developed RepurAgent, a hierarchical multi-agent AI system comprising a supervisor agent and a planning agent that coordinate four specialized sub-agents (research, prediction, data, and report), through a human-in-the-loop design, with episodic memory and retrieval-augmented generation. The system is grounded in data, tools, and standard operating procedures specific for drug repurposing, developed within the REMEDi4ALL consortium. We validated the agentic system across three scenarios spanning the various stages within the repurposing lifecycle: in Acute Myeloid Leukemia, a blinded expert evaluation indicated that RepurAgent produced substantially more novel and mechanistically credible candidates compared to a vanilla LLM baseline; in a retrospective COVID-19 antiviral screen, RepurAgent acted as an adaptive experimental collaborator, prioritizing compounds with AUC-ROC up to 0.99 without predefined thresholds and flagging confounders missed in manual review; and for Multiple Sulfatase Deficiency, it prioritized 81 high-confidence candidates from 5000 compounds, which were further corroborated by domain experts. These results demonstrate that agentic AI can support across the drug repurposing lifecycle, from hypothesis generation to experimental analysis. RepurAgent is open source and deployed at https://repuragent.serve.scilifelab.se/.

bioinformatics↗

bioRxiv2025

Lcn2 deficiency leads to social impairments independent of maternal immune activation.

Maternal infection during pregnancy is a well-established risk factor for neurodevelopmental disorders (NDDs), yet the underlying molecular mechanisms remain poorly understood. Lipocalin-2 (Lcn2), an innate immune protein that is highly upregulated during infection, also affects neuronal and glial function. This study investigates the role of Lcn2 in shaping brain development, particularly after maternal immune activation (MIA). To mimic maternal infection, pregnant mice received intraperitoneal injections of either lipopolysaccharide (LPS) or saline on embryonic days 16 to 18 to model infection during the second trimester of pregnancy in humans. We first showed that Lcn2 mRNA is expressed in the fetal brain and that MIA significantly upregulates Lcn2 mRNA and protein in the hippocampus and neocortex of both sexes. To assess functional relevance, we employed Lcn2 heterozygous females to generate wild-type and Lcn2 KO offspring from the MIA and control groups. Both female and male offspring underwent a battery of behavioral assays. Lcn2 deletion and MIA independently induced deficits in social behavior and increased repetitive behavior phenotypes relevant to NDDs in adult animals. However, their combination did not exacerbate these effects, suggesting an occlusion effect. Interestingly, no deficits were observed in the learning and memory task. To investigate potential shared molecular mechanisms, we performed RNA sequencing of the fetal forebrain 4 hours after the final LPS injection. This analysis revealed an overlapping group of differentially expressed genes in the Lcn2 KO and MIA groups, indicating convergence on similar transcriptional pathways that may underlie the observed behavioral phenotypes. These results suggest that while Lcn2 may not mediate the pathological effects of prenatal immune challenge, it plays a critical role in normal brain development.

neuroscience↗

bioRxiv2025

Spatial artefact detection improves reproducibility of drug screening experiments

Reliable and reproducible drug screening experiments are essential for drug discovery and personalized medicine. Here, we demonstrate how systematic experimental errors negatively impact reproducibility, and that conventional quality control (QC) methods based on plate controls fail to detect these errors. To address this limitation, we developed a control-independent QC approach using normalized residual fit error (NRFE) to identify systematic errors in drug screening experiments. Comprehensive analysis of >100,000 duplicate measurements from the PRISM pharmacogenomic study revealed that the NRFE-flagged experiments show three-fold lower reproducibility between technical replicates. By integrating NRFE with existing QC methods to analyze 41,762 matched drug-cell line pairs between two datasets from the Genomics of Drug Sensitivity in Cancer project, we improved the cross-dataset correlation from 0.66 to 0.76. Available as an R package at https://github.com/IanevskiAleksandr/plateQC, plateQC provides a robust toolset for enhancing drug screening data reliability and consistency for basic research and translational applications.

bioinformatics↗

bioRxiv2024

Genetic reduction of the translational repressors FMRP and 4E-BP2 preserves memory in mouse models of Alzheimer's disease

Alzheimers disease (AD) is characterized by progressive memory decline. Converging evidence indicates that hippocampal mRNA translation (protein synthesis) is defective in AD. Here, we show that genetic reduction of the translational repressors, Fragile X messenger ribonucleoprotein (FMRP) or eukaryotic initiation factor 4E (eIF4E)-binding protein 2 (4E-BP2), prevented the attenuation of hippocampal protein synthesis and memory impairment induced by AD-linked amyloid-{beta} oligomers (A{beta}Os) in mice. Moreover, genetic reduction of 4E-BP2 rescued memory deficits in aged APPswe/PS1dE9 (APP/PS1) transgenic mouse model of AD. Our findings demonstrate that strategies targeting repressors of mRNA translation correct hippocampal protein synthesis and memory deficits in AD models. Results suggest that modulating pathways controlling brain mRNA translation may confer memory benefits in AD.

neuroscience↗

bioRxiv2023

Stimulation of mRNA translation rescues hippocampal synaptic plasticity and memory in mouse models of Alzheimer's disease

Impaired synaptic plasticity and progressive memory deficits are major hallmarks of Alzheimers disease (AD). Hippocampal mRNA translation, required for memory consolidation, is defective in AD. Here, we show that systemic treatment with (2R,6R)- hydroxynorketamine (HNK), an active metabolite of the antidepressant ketamine, prevented deficits in hippocampal mRNA translation, long-term potentiation (LTP) and memory induced by AD-linked amyloid-{beta} oligomers (A{beta}Os) in mice. HNK activated hippocampal extracellular signal-regulated kinase 1/2 (ERK1/2), mechanistic target of rapamycin (mTOR), and p70S6 kinase 1 (S6K1)/ribosomal protein S6 (S6), which promote protein synthesis and synaptic plasticity. Stimulation of S6 phosphorylation by HNK was mTORC1-dependent, while rescue of hippocampal LTP and memory in HNK-treated A{beta}O-infused mice was ERK1/2-dependent and, partially, mTORC1- dependent. Remarkably, treatment with HNK corrected LTP and memory deficits in aged APP/PS1 mice. Transcriptomic analysis further showed that HNK rescued signaling pathways that are aberrant in APP/PS1 mice, including inflammatory and hormonal responses, and programmed cell death. Taken together, our findings demonstrate that HNK induces signaling and transcriptional responses that correct deficits in hippocampal synaptic plasticity and memory in AD mouse models. These results raise the prospect that HNK could serve as a therapeutic to prevent or reverse memory decline in AD.

neuroscience↗

bioRxiv2023

Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones

Intratumoral cellular heterogeneity necessitates multi-targeting therapies for improved clinical benefits in patients with advanced malignancies. However, systematic identification of patient-specific treatments that selectively co-inhibit cancerous cell populations poses a combinatorial challenge, since the number of possible drug-dose combinations vastly exceeds what could be tested in scarce patient cells. Here, we developed scTherapy, a machine learning model that leverages single-cell transcriptomic profiles to prioritize multi-targeting treatment options for individual patients with hematological cancers or solid tumors.

bioinformatics↗

bioRxiv2023

Excitatory neuron-specific suppression of the integrated stress response pathway contributes to autism-related phenotypes in a mouse model of fragile X syndrome

Dysregulation of protein synthesis is one of the key mechanisms underlying autism spectrum disorder (ASD). However, the role of a major pathway controlling protein synthesis, the integrated stress response (ISR), in ASD remains poorly understood. Here, we demonstrate that the main arm of the ISR, eIF2 phosphorylation (p-eIF2), is suppressed in excitatory but not inhibitory neurons in a mouse model of fragile X syndrome (FXS; Fmr1-/y). We further show that the decrease in p-eIF2 is mediated via activation of the mTORC1. Genetic reduction of p-eIF2 only in excitatory neurons is sufficient to increase general protein synthesis and cause autism-like behavior. In Fmr1-/y mice, genetic restoration of p-eIF2 solely in excitatory neurons reverses elevated protein synthesis and rescues autism-related phenotypes. Thus, we reveal a previously unknown causal relationship between excitatory neuron-specific translational control via the ISR pathway, general protein synthesis and core phenotypes reminiscent of autism in a mouse model of FXS.

neuroscience↗

bioRxiv2023

Network-Level Changes in the Brain Underlie Fear Memory Intensity

The strength of a fear memory significantly influences whether it drives adaptive or maladaptive behavior in the future. Yet, how mild and strong fear memories differ in underlying biology is not well understood. We hypothesized that this distinction may not be exclusively the result of changes within specific brain regions, but rather the outcome of collective changes in connectivity across multiple regions within the neural network. To test this, rats were fear conditioned in protocols of varying intensities to generate mild or strong memories. Neuronal activation driven by recall was measured using c-fos immunohistochemistry in 12 brain regions implicated in fear learning and memory. The interregional coordinated brain activity was computed and graph-based functional networks were generated to compare how mild and strong fear memories differ at the systems level. Our results show that mild fear recall is supported by a well-connected brain network with small-world properties in which the amygdala is well-positioned to be modulated by other regions. In contrast, this connectivity is disrupted in strong fear memories and the amygdala is isolated from other regions. These findings indicate that the neural systems underlying mild and strong fear memories differ, with implications for understanding and treating disorders of fear dysregulation.

neuroscience↗

bioRxiv2020

Serum response factor is essential for synaptic maturation in the hippocampus

Disturbances of gene expression patterns that occur during brain development can severely affect signal transmission, connectivity, and plasticity--key features that underlie memory formation and storage in neurons. Abnormalities at the molecular level can manifest as changes in the structural and functional plasticity of dendritic spines that harbor excitatory synapses. This can lead to such developmental neuropsychiatric conditions as Autism spectrum disorders, intellectual disabilities, and schizophrenia. The present study investigated the role of the major transcriptional regulator serum response factor (SRF) in synapse maturation and its impact on behavioral phenotypes. Using in vitro and in vivo models of early postnatal SRF deletion, we studied its influence on key morphological and physiological hallmarks of spine development. The elimination of SRF in developing neurons resulted in a phenotype of immature dendritic spines and impairments in excitatory transmission. Moreover, using a combination of molecular and imaging techniques, we showed that SRF-depleted neurons exhibited a lower level of specific glutamate receptor mRNAs and a decrease in their surface expression. Additionally, the early postnatal elimination of SRF in hippocampal CA1 excitatory neurons caused spine immaturity and a specific social deficit that is frequently observed in autism patients. Altogether, our data suggest that the regulation of structural and functional dendritic spine maturation begins at the stage of gene transcription, which underpins the crucial role of such transcription factors as SRF. Moreover, disturbances of the postnatal expression of SRF translate to behavioral changes in adult animals.

neuroscience↗

bioRxiv2020

Memory destabilization and reconsolidation dynamically regulate the PKMζ maintenance mechanism

Useful memory must balance between stability and malleability. This puts effective memory storage at odds with plasticity processes like reconsolidation. What becomes of memory maintenance processes during synaptic plasticity is unknown. Here we examined the fate of the memory maintenance protein PKM{zeta} during memory destabilization and reconsolidation. We found that NMDA receptor activation and proteasome activity induced a transient reduction in PKM{zeta} protein following retrieval. During reconsolidation, new PKM{zeta} was synthesized to re-store the memory. Failure to synthesize new PKM{zeta} during reconsolidation impaired memory but uninterrupted PKM{zeta} translation was not necessary for maintenance itself. Finally, NMDA receptor activation was necessary to render memories vulnerable to the amnesic effect of PKM{zeta}-antisense. These findings outline a transient collapse and renewal of the PKM{zeta} memory maintenance mechanism during plasticity. We argue that dynamic changes in PKM{zeta} protein levels can serve as an exemplary model of the molecular changes underlying memory destabilization and reconsolidation.

neuroscience↗

bioRxiv2020

Noradrenergic projections from the locus coeruleus to the amygdala constrain auditory fear memory reconsolidation

Memory reconsolidation is a fundamental plasticity process in the brain that allows established memories to be changed or erased. However, certain boundary conditions limit the parameters under which memories can be made plastic. Strong memories do not destabilize, for instance, although why they are resilient is mostly unknown. Here, we extend the understanding of the mechanisms implicated in reconsolidation-resistant memories by investigating the hypothesis that specific modulatory signals shape memory formation into a state that lacks lability. We find that the activation of the noradrenaline-locus coeruleus system (NOR-LC) during strong fear memory encoding increases molecular mechanisms of stability at the expense of lability in the amygdala. Preventing the NOR-LC from modulating strong fear encoding results in the formation of memories that can undergo reconsolidation within the amygdala and thus are vulnerable to post-reactivation interference. Thus, the memory strength boundary condition on reconsolidation is set at the time of encoding by the action of the NOR-LC.

neuroscience↗