Biology subjects

Roopra, A.

Publications and source records attributed to Roopra, A..

9 recordsLinked to original sources

bioRxiv2026

JAK inhibition overcomes first-line drug resistance in a pre-clinical model of epilepsy

One-third of people with epilepsy continue to have seizures despite antiseizure medications (ASMs), and available therapies often fail to improve disabling cognitive comorbidities. Patients with drug resistant epilepsy report that the adverse effects of medications along with their comorbidities can have a greater negative impact on the quality of life than seizures. We previously identified recurrent JAK/STAT3 activation in chronic epilepsy and showed that transient treatment with the JAK inhibitor tofacitinib (CP690550) durably suppresses seizures and restores cognition in mice. Here, we tested CP690550 as an add-on therapy after failure of carbamazepine (CBZ), a common first line treatment for epilepsy, in a mouse model of multifocal temporal lobe epilepsy. In CBZ-resistant animals, dual therapy with CP690550 reduced median seizure frequency and time spent seizing by an order of magnitude; most dual therapy responders had no observed behavioral seizures during treatment. CP690550 also restored spatial working and short-term memory. We found that cognitive rescue was independent of seizure response. Our work suggests that JAK/STAT inhibition can overcome ASM nonresponse while independently improving epilepsy-associated cognitive dysfunction.

neuroscience↗

bioRxiv2026

H3K27me3 maintains baseline network excitability after status epilepticus

The processes by which epileptic insults precipitate the molecular, cellular, and network alterations in the brain that lead to epilepsy are poorly understood. We previously discovered that after status epilepticus (SE - an epilepsy inducing severe bout of seizures) the H3K27 methylase Enhancer of Zeste Homolog 2 (EZH2) is robustly induced and drives repression of genes. Both systemic pharmacological inhibition of EZH2 and deletion of EZH2 in neurons exacerbates epilepsy progression, suggesting that acute EZH2 induction may exert a net protective effect against disease progression chronically. However, the mechanisms underlying EZH2-mediated control of the putative protective and pathological pathways in disease progression are still unknown. To interrogate the mechanisms of EZH2 function post-SE, we used bulk CUT&RUN- sequencing against H3K27me3 in tandem with bulk RNA-sequencing in hippocampi of naive and 4d. post-SE mice to profile epigenomic and transcriptomic changes. Differential peak analysis showed that H3K27me3 was enriched both at loci pre-marked by H3K27me3 in the naive hippocampus as well as in loci that were de novo methylated after SE, consistent with the SE-dependent induction of EZH2 protein levels. Multi-omic integration of CUT&RUN and RNA-seq data revealed a module of genes that were coordinately H3K27me3 enriched, transcriptionally repressed, and annotated to ontological terms involved in neuronal signaling and network excitability. This result suggests that EZH2 induction may function in part to control network excitability after injury. To test this, we treated mice acutely post-SE with the EZH2 inhibitor UNC1999 and found that EZH2 inhibition attenuated H3K27me3 induction and dampened repression of target network excitability genes in response to SE. Functionally, UNC1999 treatment significantly increased seizure probability acutely and exacerbated disease severity in the chronic period. Taken together, these results suggest that EZH2 induction after injury may function to maintain network excitability to lower seizure probability acutely to protect against disease progression.

neuroscience↗

bioRxiv2023

Tofacitinib effects profound seizure suppression through mimicking EZH2 antagonism of a pro-inflammatory gene network in epilepsy.

All current drug treatments for epilepsy, a neurological disorder affecting over 50 million people(1, 2) merely treat symptoms, and a third of patients do not respond to medication. There are no disease modifying treatments that may be administered briefly to patients to enduringly eliminate spontaneous seizures and reverse cognitive deficits(3, 4). Applying network approaches to rodent models and human temporal lobectomy samples at both whole tissue and single-nuclei resolutions, we observe the well-characterized pattern of rapid induction and subsequent quenching exhibited of the JAK/STAT pathway within days of epileptogenic insult. This is followed by a resurgent activation weeks to months later with the onset of spontaneous seizures. Targeting the first wave of activation after epileptic insult does not prevent disease. However, brief inhibition of the second wave with CP690550 (Tofacitinib) (5, 6) enduringly suppresses seizures, rescues deficits in spatial memory, and alleviates epilepsy-associated histopathological alterations. Seizure suppression lasts for at least 2 months after the final dose. Using discovery-based transcriptomic analysis across models of epilepsy and validation of putative mechanisms with human data, we demonstrate a powerful approach to identifying disease modifying targets; this may be useful for other neurological disorders. With this approach, we find that reignition of inflammatory JAK/STAT3 signaling in chronic epilepsy opens a window for disease modification with the FDA-approved, orally available drug CP690550.

neuroscience↗

bioRxiv2022

Recurrent hypoxia in a rat model of sleep apnea during pregnancy leads to microglia-dependent respiratory deficits and persistent neuroinflammation in adult male offspring

Sleep apnea (SA) during pregnancy is detrimental to the health of the pregnancy and neonate, but little is known regarding long-lasting consequences of maternal SA during pregnancy on adult offspring. SA is characterized by repeated cessations in breathing during sleep, resulting in intermittent hypoxia (IH). We show that gestational IH (GIH) in rats reprograms the male fetal neuroimmune system toward enhanced inflammation in a region- and sex-specific manner, which persists into adulthood. Male GIH offspring also had deficits in the neural control of breathing, specifically in the ability to mount compensatory responses to central apnea, an effect that was rescued by a localized anti-inflammatory or microglial depletion. Female GIH offspring appeared unaffected. These results indicate that SA during pregnancy sex- and region-dependently skews offspring microglia toward a pro-inflammatory phenotype, which leads to long-lasting deficits in the capacity to elicit important forms of respiratory neuroplasticity in response to breathing instability. These studies contribute to the growing body of recent evidence indicating that SA during pregnancy may lead to sex-specific neurological deficits in offspring that persist into adulthood.

neuroscience↗

bioRxiv2022

Autofluorescence is a biomarker of neural stem cell activation state

Neural stem cells (NSCs) in the adult brain are primarily quiescent but can activate and enter the cell cycle to produce newborn neurons. NSC quiescence can be regulated by disease, injury, and age, however our understanding of NSC quiescence is limited by technical limitations imposed by the bias of markers used to isolate each population of NSCs and the lack of live-cell labeling strategies. Fluorescence lifetime imaging (FLIM) of autofluorescent metabolic cofactors has previously been used in other cell types to study shifts in cell states driven by metabolic remodeling that change the optical properties of these endogenous fluorophores. Here we asked whether autofluorescence could be used to discriminate NSC activation state. We found that quiescent NSCs (qNSCs) and activated NSCs (aNSCs) each have unique autofluorescence intensity and fluorescence lifetime profiles. Additionally, qNSCs specifically display an enrichment of a specific autofluorescent signal localizing to lysosomes that is highly predictive of cell state. These signals can be used as a graded marker of NSC quiescence to predict cell behavior and track the dynamics of quiescence exit at single cell resolution in vitro and in vivo. Through coupling autofluorescence imaging with single-cell RNA sequencing in vitro and in vivo, we provide a high-resolution resource revealing transcriptional features linked to rapid NSC activation and deep quiescence. Taken together, we describe a single-cell resolution, non-destructive, live-cell, label-free strategy for measuring NSC activation state in vitro and in vivo and use this tool to expand our understanding of adult neurogenesis.

neuroscience↗

bioRxiv2020

Prior hypoxia exposure enhances murine microglial inflammatory gene expression in vitro without concomitant H3K4me3 enrichment

Hypoxia is a component of multiple disorders, including stroke and sleep-disordered breathing, that often precede or are comorbid with neurodegenerative diseases. However, little is known about how hypoxia affects the ability of microglia, resident CNS macrophages, to respond to subsequent inflammatory challenges that are often present during neurodegenerative processes. We therefore tested the hypothesis that hypoxia would enhance or "prime" microglial pro-inflammatory gene expression in response to a later inflammatory challenge without programmatically increasing basal levels of pro-inflammatory cytokine expression. To test this, we pre-exposed immortalized N9 and primary microglia to hypoxia (1% O2) for 16 hrs and then challenged them with pro-inflammatory lipopolysaccharide (LPS) either immediately or 3-6 days following hypoxic exposure. We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to analyze primed microglial inflammatory gene expression and modifications to histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of primed genes. We found that microglia exhibited enhanced responses to LPS 3 days and 6 days post-hypoxia. Surprisingly however, the majority of primed genes were not enriched for H3K4me3 acutely following hypoxia exposure. Using the bioinformatics tool MAGICTRICKS and reversible pharmacological inhibition, we found that primed genes required the transcriptional activities of NF-B. These findings provide evidence that hypoxia pre-exposure could lead to persistent and aberrant inflammatory responses in the context of CNS disorders.

neuroscience↗

bioRxiv2019

A Systems Approach Identifies Enhancer of Zeste Homolog 2 (EZH2) as a Protective Factor in Epilepsy

Complex neurological conditions can give rise to large scale transcriptomic changes that drive disease progression. It is likely that alterations in one or a few transcription factors or cofactors underlie these transcriptomic alterations. Identifying the driving transcription factors/cofactors is a non-trivial problem and a limiting step in the understanding of neurological disorders. Epilepsy has a prevalence of 1% and is the fourth most common neurological disorder. While a number of anti-seizure drugs exist to treat seizures symptomatically, none is curative or preventive. This reflects a lack of understanding of disease progression. We used a novel systems approach to mine transcriptome profiles of rodent and human epileptic brain samples to identify regulators of transcriptional networks in the epileptic brain. We find that Enhancer of Zeste Homolog 2 (EZH2) regulates differentially expressed genes in epilepsy across multiple rodent models of acquired epilepsy. EZH2 undergoes a prolonged upregulation in the epileptic brain. A transient inhibition of EZH2 immediately after seizure induction robustly increases spontaneous seizure burden weeks later. Thus, EZH2 upregulation is a protective response mounted after a seizure. These findings are the first to characterize a role for EZH2 in opposing epileptogenesis and debut a bioinformatic approach to identify nuclear drivers of complex transcriptional changes in disease.\n\nAuthor SummaryEpilepsy is the fourth most common neurological disorder and has been described since the time of Hippocrates. Despite this, no treatments exist to stop epilepsy progression. This is fundamentally due to the complex nature of the disease. Epilepsy is associated with hundreds if not thousands of gene expression changes in the brain that are likely driven by a few key master regulators called transcription factors and cofactors. Finding the aberrantly acting factors is a complex problem that currently lacks a satisfactory solution. We used a novel datamining tool to define key master regulators of gene expression changes across multiple epilepsy models and patient samples. We find that a nuclear enzyme, EZH2, regulates a large number of genes in the rodent and patient epileptic brain and that its function is protective. Thus, inhibiting EZH2 greatly exacerbates seizure burden. This is the first report of a novel datamining tool to define drivers of large-scale gene changes and is also the first report of EZH2 induction as an endogenous protective response in the epilepsy.

neuroscience↗

bioRxiv2018

MAGIC: A tool for predicting transcription factors and cofactors binding sites in gene sets using ENCODE data.

Transcriptomic profiling is an immensly powerful hypothesis generating tool. Whether one is comparing an experimental versus control condition or collecting transcriptomes from cohorts of disease tissue, it is often necessary to determine which transcription factors (TFs) and cofactors drive programs of gene expression in the datasets. Most available tools rely on searching for TF binding motifs near promoters of genes in a gene set. This approach can work well for TFs with extended recognition elements but is less useful for shorter elements and does not work at all for cofactors. The Encyclopedia Of DNA Elements (ENCODE) archives ChIPseq tracks of 169 TFs and cofactors assayed in 91 cells lines. The algorithm presented herein, Multiple Aligned Genomic Integration of ChIP (MAGIC), uses ENCODE ChIPseq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene sets. When compared to a commonly used web resource o-Possum, MAGIC was able to more accurately predict TFs and cofactors that drive gene changes in 3 settings: 1) A cell line expressing or lacking REST, 2) Breast tumors divided along PAM50 designations and 3) Whole brain samples from WT mice or mice lacking CTCF in a particular neuronal subtype. In summary, MAGIC is a standalone application that runs on OSX machines and has a simple interface that produces meaningful predictions of which TFs and cofactors are enriched in a gene set.

bioinformatics↗

bioRxiv2017

Tonic Inhibition is Abolished in GABAA Receptor γ2R43Q Knock-in Mice with Absence Epilepsy and Febrile Seizures.

The {gamma}2R43Q GABAA receptor mutation confers absence epilepsy in humans, and {gamma}2R43Q knock-in mice (RQ) display absence seizures and generalized spike-and-wave discharges reminiscent of their human counterparts. Previous work on several rodent models led to the conclusion that elevated tonic inhibition in thalamic neurons is necessary and sufficient to produce typical absence epilepsy. In contrast, here we used patch-clamp electrophysiology in brain slices to show that RQ mice entirely lack tonic inhibition in principal cells of layer II/III somatosensory cortex and ventrobasal thalamus. Additionally, protein quantification and multielectrode electrophysiology show that the mutation interferes with trafficking of GABAA receptor subunits involved in generating tonic currents, leading to increased cortical firing and decreased thalamic bursting rates. Together with previous work, our results suggest that an optimum level of tonic inhibition is required for normal thalamocortical function, such that deviations in either direction away from this optimum enhance susceptibility to absence seizures.

neuroscience↗