Biology subjects

Bahari, F.

Publications and source records attributed to Bahari, F..

5 recordsLinked to original sources

bioRxiv2026

Cancer Driver Gene Discovery: A Patient-Level Statistical Framework

Tumor genomes harbor a mixture of neutral and positively selected mutations, yet distinguishing true cancer drivers remains a major challenge. Several factors can obscure the detection of selection signals, among which patient-specific variation in mutational burden plays a significant role. Current approaches often fail to account for the heterogeneity in mutation burden across different patients; in particular, no existing method explicitly accounts for it when integrating both mutation recurrence and functional impact. Here we present iDriver, a probabilistic graphical model that integrates both mutation recurrence and functional impact at the individual-patient level, enabling an enhanced estimation of positive selection across functional genomic elements. Applying iDriver to 29 cancer types, we identify both known and previously unrecognized drivers spanning coding and noncoding regions, and provide evidence for their clinical and biological relevance. In comprehensive benchmarks against 12 established driver discovery methods, iDriver consistently outperformed all competitors, achieving the highest rankings for known cancer drivers across both coding and noncoding elements.

bioinformatics↗

bioRxiv2023

A dynamic balance between neuronal death and clearance after acute brain injury

After acute brain injury, neuronal apoptosis may overwhelm the capacity for microglial phagocytosis, creating a queue of dying neurons awaiting clearance. The size of this queue should be equally sensitive to changes in neuronal death and the rate of phagocytosis. Using rodent organotypic hippocampal slice cultures as a model of acute perinatal brain injury, serial imaging demonstrated that the capacity for microglial phagocytosis of dying neurons was overwhelmed for two weeks. Altering phagocytosis rates, e.g. by changing the number of microglia, dramatically changed the number of visibly dying neurons. Similar effects were generated when the visibility of dying neurons was altered by changing the membrane permeability for vital stains. Canonically neuroprotective interventions such as seizure blockade and neurotoxic maneuvers such as perinatal ethanol exposure were mediated by effects on microglial activity and the membrane permeability of apoptotic neurons, and had either no or opposing effects on healthy surviving neurons. SignificanceAfter acute brain injury, microglial phagocytosis is overwhelmed by the number of dying cells. Under these conditions, the assumptions on which assays for neuroprotective and neurotoxic effects are based are no longer valid. Thus longitudinal assays of healthy cells, such as assessment of the fluorescence emission of transgenically-expressed proteins, provide more accurate estimates of cell death than do single-time-point anatomical or biochemical assays. More accurate estimates of death rates will increase the translatability of preclinical studies of neuroprotection and neurotoxicity.

neuroscience↗

bioRxiv2022

The Functional Landscape of SARS-CoV-2 3CL Protease

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as the etiologic agent of COVID-19 (coronavirus disease 2019) has drastically altered life globally. Numerous efforts have been placed on the development of therapeutics to treat SARS-CoV-2 infection. One particular target is the 3CL protease (3CLpro), which holds promise as it is essential to the virus and highly conserved among coronaviruses, suggesting that it may be possible to find broad inhibitors that treat not just SARS-CoV-2 but other coronavirus infections as well. While the 3CL protease has been studied by many groups for SARS-CoV-2 and other coronaviruses, our understanding of its tolerance to mutations is limited, knowledge which is particularly important as 3CL protease inhibitors become utilized clinically. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the SARS-CoV-2 3CLpro, and validate our results both in yeast and in authentic viruses. We reveal that the 3CLpro is highly malleable and is capable of tolerating mutations throughout the protein, including within the substrate binding pocket. Yet, we also identify specific residues that appear immutable for function of the protease, suggesting that these interactions may be novel targets for the design of future 3CLpro inhibitors. Finally, we utilize our screening results as a basis to identify E166V as a resistance-conferring mutation against the therapeutic 3CLpro inhibitor, nirmatrelvir, in clinical use. Collectively, the functional map presented herein may serve as a guide for further understanding of the biological properties of the 3CL protease and for drug development for current and future coronavirus pandemics.

microbiology↗

bioRxiv2020

Probing Causality of the Brainstem-Hypothalamic Murine Models of Sleep-Wake Regulation

Sleep-wake regulation is thought to be governed by interactions among several nuclei in midbrain, pons, and hypothalamic regions. Determination of the causal role of these nuclei in state transitions requires simultaneous measurements from the nuclei with sufficient spatial and temporal resolution. We obtained long-term experimental single- and multi-unit measurements simultaneously from multiple nuclei of the putative hypothalamic and brainstem sleep-wake regulatory network in freely behaving rats. Cortical and hippocampal activity, along with head acceleration were also acquired to assess behavioral state. Here, we confirm that the general activity profile of the recorded sleep-wake regulatory nuclei is similar to the patterns presented previously in brief recordings of individual nuclei in head-fixed animals. However, we found that these activity profiles when studied with respect to cortical and behavioral signs of state transitions differ significantly from previous reports. Our findings pose fundamental questions about the neural mechanisms that maintain specific states and the neural interactions that lead to the emergence of sleep-wake states.

neuroscience↗

bioRxiv2018

Spreading Depression and Seizure Unification Experimentally Observed in Epilepsy

Spreading depression is characterized by slow, propagating wave of cellular depolarization (SD) and is wildly associated with migraine, stroke, and traumatic brain injury. Seizures and spreading depression (or spreading depolarization, SD) have long been reported to coincide in acute seizure induction experiments. However, SD has not been observed associated with spotaneous seizures in animal or clinical recordings. Recently, advances in acquisition systems for neurointensive care units have made routine observations of SD possible. In clinical epilepsy, SD has been suggested as a candidate mechanism for migraine/headache like events following seizures as well as for post-ictal generalized suppression. In animal models of epilepsy, seizure-induced brainstem SD has also been demonstrated as a mechanism of sudden unexplained death in epilepsy (SUDEP). The interplay between seizures and SD has also been suggested in computational models, where the two are components of the repetoir of neuronal activity. However, the spatiotemporal dynamics of SD with respect to spontaneous seizures in chronically epileptic brain remains ambigous. We analyzed continuous long-term DC sensitive EEG measurements from two fundamentally different animal models of chronic epilepsy. We found that SD was associated with approximately one-third of all spontaneous seizures in each model. Additionally, SDs participated in the organization of seizure clusters. These findings demonstrate that the underlying dynamic of epileptic events is broader than seizures alone. Significance StatementSpreading depression is characterized by slow, propagating wave of cellular spreading depolarization (SD) and is wildly associated with migraine, stroke, and traumatic brain injury. Although recently the linkage between SD and induced seizures has been recognized, the mechanistic relationship between SD and spontaneous seizures remains poorly understood. Here, we utilized long-term, stable, near-DC measurements of the brain activity in two fundamentally different animal models of epilepsy to investigate the SD-seizure interplay. We found that SD is a frequent phenomenon in the epileptic brain, in these models is associated with more than a third of all seizures, and appears to connect seizures in seizure clusters. Although in one model SD stereotypically propagates out from a single focus in the hippocampus, depression of the field-potentials is observed synchronously across much of the hippocampus. These observations highlight the value of stable DC measurements for accurate understanding of SD and its propagation. We found that spontaneous ictal events that include both seizures and SD are frequent in animal models of epilepsy. These findings suggest that SD could be a valuable target for treatment and control of epilepsy.

neuroscience↗