Biology subjects

Heller, E. A.

Publications and source records attributed to Heller, E. A..

15 recordsLinked to original sources

bioRxiv2026

Systemic stress states are reversed by NPBWR1 inhibition

Chronic stress is widely studied as a brain-centered driver of depression, yet its effects across the body remain unclear. Here, we define chronic stress as a coordinated molecular state across tissues in mice. Using a whole-body proteomic atlas of 13 tissues, we find that stress effects are strongest in peripheral metabolic and endocrine organs, whereas classical stress-associated brain regions show comparatively modest changes. Cross-organ analyses reveal structured, tissue-specific responses rather than uniform shifts. Inhibition of the stress-regulated receptor NPBWR1 reverses both behavioral deficits and proteomic alterations across organs in both sexes, indicating that this state is dynamically modifiable. Integration with human serum proteomics identifies shared, sex-specific signatures. Across tissues, lipid metabolism emerges as a common stress-responsive pathway, confirmed by hepatic lipid remodeling that is normalized by NPBWR1 inhibition. To facilitate exploration of these data, we provide an interactive cross-organ web-based resource. Together, these findings challenge the brain-centric view of stress pathology and define chronic stress as an organism-wide molecular state.

systems biology↗

bioRxiv2026

Neuron-specific epigenetic repression of Cdk5 impairs hippocampal-dependent memory in male and female mice

Biological sex regulates fundamental neurobiology, as well as the etiology and prevalence of neuropsychiatric disorders. Cyclin-dependent kinase 5 (Cdk5) is a neuronally enriched kinase that regulates synaptic plasticity, neuronal homeostasis, and hippocampal-dependent memory. While Cdk5 protein activity is necessary and sufficient to promote memory in male rodents, its role in females and its gene regulation in either sex remain poorly understood. In males, Cdk5 protein inhibition impairs fear memory. We previously showed that fear conditioning activates Cdk5 gene expression and increases permissive chromatin acetylation in male, but not female hippocampus. We hypothesize that Cdk5 gene repression would impair fear memory in males. We developed an excitatory neuron-specific, CRISPR/dCas9-HDAC3 epigenetic editing tool to target histone acetylation at the endogenous Cdk5 promoter. This strategy reduced histone acetylation and decreased Cdk5 mRNA, protein, and kinase activity in both sexes. Interestingly, Cdk5 repression in hippocampal neurons impaired fear and spatial memory in both male and female mice. Targeted deacetylation also evicted the transcription factor CREB1 from the Cdk5 promoter, revealing a link between histone acetylation and Cdk5 transcriptional activation. These findings demonstrate that Cdk5 acetylation in neurons is necessary for hippocampal memory in both sexes, providing new insight into sex-specific epigenetic regulation of memory.

molecular biology↗

bioRxiv2025

Hippocampal Cdk5 is regulated by distinct stress paradigms in male and female mice

Anxiety and mood disorders have been rising since the COVID-19 pandemic, marked by social isolation and stress. Women are disproportionately affected by stress-related disorders, yet the interaction between social isolation and stress remains understudied in females. Cyclin-dependent kinase 5 (Cdk5) is an atypical kinase that exhibits sex-specific regulation following various stressors but is studied almost exclusively in males. To complement these findings, we examined sex differences in mouse hippocampal Cdk5 mRNA and protein following short and long restraint stress with or without concomitant social isolation stress. While short restraint stress was sufficient to promote anxiety-like in both male and female mice, it did not alter Cdk5. Rather, hippocampal Cdk5 mRNA increased only after a longer restraint stress duration followed by social isolation, and only in male mice. Hippocampal Cdk5 protein also shifted from the cytosolic to the nuclear compartment only in male hippocampus. Surprisingly, repeated restraint stress promoted exploratory behavior in both group-housed and socially isolated male and female mice. Social isolation alone increased Cdk5 protein in females only. Finally, under all conditions, female mice were less immobile and more exploratory than male mice. Together, these results provide new insight into the sex-specific regulation of hippocampal Cdk5 by the combination of psychological and environmental stressors. HighlightsO_LIShort 10-minute restraint stress induced anxiety-like behavior in both sexes without altering hippocampal Cdk5 expression. C_LIO_LILong 1-hour restraint stress with post-stress social isolation elicited male-specific hippocampal Cdk5 transcription and Cdk5 cytosolic-to-nuclear protein redistribution. C_LIO_LIRepeated restraint stress increased exploratory behavior in both sexes, suggesting altered stress responsiveness. C_LIO_LISocial isolation interacted with repeated restraint to alter hippocampal Cdk5 protein levels selectively in females. C_LI

neuroscience↗

bioRxiv2025

Epigenetic editing of Cartpt promotes acquisition and extinction of cocaine memory

In classic disease models, removing a pathological insult restores homeostasis. Yet, addiction persists far beyond the period of active drug use. Cocaine abstinence induces changes in gene expression and neuronal signaling in reward-related brain regions that limit recovery during abstinence. We found that 2 weeks of abstinence increased Cartpt (cocaine- and amphetamine-regulated transcript) in the mouse nucleus accumbens and decreased repressive H3K27me3 at the Cartpt locus. While endogenous CART peptide is best described for its anorexigenic function, it is also implicated in human addiction and dopamine homeostasis. To test the causal relevance of Cartpt chromatin remodeling, we used CRISPR-based epigenetic editing tools, dCas9-FOG1 and dCas9-JMJC-ZF, to manipulate H3K27me3 at Cartpt in vivo. Enriching H3K27me3 in D1 neurons repressed Cartpt expression and augmented acquisition and extinction of cocaine preference. These results show that CRISPR epigenetic editing can recapitulate endogenous chromatin states to modulate addiction-related behavior, highlighting broad therapeutic potential of both Cartpt and epigenetic editing. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/689329v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1b84229org.highwire.dtl.DTLVardef@1ffc2d7org.highwire.dtl.DTLVardef@50cf00org.highwire.dtl.DTLVardef@1462d10_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

CRISPR-mediated transcriptional activation as a mutation-independent therapeutic strategy for SYNGAP1-related intellectual disability

Synaptic Ras GTPase-activating protein (SynGAP) regulates synaptic strength and neuronal signaling, with essential roles in cortical development and synaptic plasticity. Heterozygous loss-of-function variants in SYNGAP1 cause SYNGAP1-related intellectual disability (SRID), a severe neurodevelopmental disorder characterized by epilepsy, developmental delay, and autism. SYNGAP1 mutations often result in haploinsufficiency, providing a strong rationale for gene-targeted therapies. However, no treatment currently addresses the underlying genetic cause of SRID. Here, we developed a CRISPR-mediated transcriptional activation (CRISPRa) approach to upregulate the functional Syngap1 allele in a SRID mouse model. CRISPRa activated Syngap1, normalized SynGAP protein expression and downstream signaling, and rescued working memory deficits. We validated the translational potential of this strategy in human induced pluripotent stem cell (hiPSC)-derived excitatory cortical neurons. CRISPRa rescued SYNGAP1 in two distinct loss-of-function variant lines. Together, these findings demonstrate the feasibility of mutation-independent transcriptional activation as a therapeutic approach for SRID and its broader applicability to haploinsufficiency disorders.

neuroscience↗

bioRxiv2025

Corticosterone drives behavioral inflexibility via plasticity-related gene expression in the dorsal striatum

Behavioral flexibility allows organisms to modify actions based on new information, such as shifts in reward value or availability, and is promoted by the dorsomedial striatum (DMS). In contrast, behavioral inflexibility provides efficiency and automaticity in familiar contexts, and is promoted by the dorsolateral striatum (DLS). Importantly, chronic elevation of the primary stress hormone, corticosterone (CORT) in rodents or cortisol in humans, impairs behavioral flexibility through dendritic atrophy in the DMS, and promotes inflexible behavioral response strategies through dendritic outgrowth in the DLS. However, understanding of the molecular mechanisms that underlie the structural changes promoting behavioral inflexibility is lacking. We used a food-motivated operant task in male and female mice to define synaptic plasticity gene regulation supporting a decreased DMS activity and increased DLS activity in the shift to inflexible behavior with CORT. We discovered that CORT-accelerated loss of behavioral flexibility is accompanied by decreased DMS- and increased DLS-specific synaptic plasticity gene expression, and that distinct genes are either differentially expressed or spliced in the transition to inflexible behavior. Splicing analysis suggests that repressed activity in the DMS during the transition to inflexible behavior reflects both reduced expression and increased degradation of plasticity-related mRNA transcripts. Finally, given the ability of CORT to influence histone acetylation, we defined CORT-mediated H3K9ac enrichment profiles associated with synaptic plasticity gene regulation stratified by sex and striatal subregion. This study is the first to define CORT-driven epigenetic regulation in the DMS and DLS during the transition from flexible to inflexible behavior in male and female mice.

neuroscience↗

bioRxiv2025

Unexpected mechanisms of sex-specific memory vulnerabilities to acute traumatic stress

It is increasingly recognized that severe acute traumatic events (e.g., mass shooting, natural disasters) can provoke enduring memory disturbances, and these problems are more common in women. We probed the fundamental sex differences underlying memory vulnerability to acute traumatic stress (ATS), focusing on the role of the sex hormone, estrogen (17{beta}-estradiol) and its receptor signaling in hippocampus. Surprisingly, high physiological hippocampal estrogen levels were required for ATS-induced episodic memory disruption and the concurrent sensitization and generalization of fear memories in both male and female mice. Pharmacological and transgenic approaches demonstrated signaling via estrogen receptor (ER) in males and, in contrast, ER{beta} in females, as the mechanisms for these memory problems. Finally, identify distinct hippocampal chromatin states governed by sex and estrogen levels, which may confer an enduring vulnerability to post-traumatic memory disturbances in females.

neuroscience↗

bioRxiv2024

Transthyretin orchestrates vitamin B12-induced stress resilience

Chronic stress significantly contributes to mood- and anxiety disorders. Previous and current data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood. This study reveals a molecular pathway that functionally connects vitamin B12, DNA methylation (DNAme), and stress resilience. We identified Transthyretin (Ttr) as a sex-specific key target of vitamin B12 action in chronic stress. Accordingly, TTR expression was increased postmortem in the prefrontal cortex of male, but not female, depressed patients. Virally altered Ttr in the prefrontal cortex functionally contributed to stress- and depression-related behaviors, changes in dendritic spine morphology and gene expression. In stressed mice, vitamin B12 reduced DNAme in the Ttr promoter region. Importantly, using in vivo epigenome editing to alter DNAme in the brains of living mice for the first time, we establish a direct causal link between DNAme on Ttr and stress-associated behaviors. In summary, using state-of-the-art techniques, this study uncovers a mechanistic link between cobalamin supplementation and markers of chronic stress and depression, encouraging further studies into environmental interventions for mood disorders.

neuroscience↗

bioRxiv2024

Psilocybin-enhanced fear extinction linked to bidirectional modulation of cortical ensembles

The serotonin 2 receptor (5HT2R) agonist psilocybin displays rapid and persistent therapeutic efficacy across neuropsychiatric disorders characterized by cognitive inflexibility. However, the impact of psilocybin on patterns of neural activity underlying sustained changes in behavioral flexibility has not been characterized. To test the hypothesis that psilocybin enhances behavioral flexibility by altering activity in cortical neural ensembles, we performed longitudinal single-cell calcium imaging in the retrosplenial cortex across a five-day trace fear learning and extinction assay. A single dose of psilocybin induced ensemble turnover between fear learning and extinction days while oppositely modulating activity in fearand extinctionactive neurons. The acute suppression of fear-active neurons and delayed recruitment of extinction-active neurons were predictive of psilocybin-enhanced fear extinction. A computational model revealed that acute inhibition of fear-active neurons by psilocybin is sufficient to explain its neural and behavioral effects days later. These results align with our hypothesis and introduce a new mechanism involving the suppression of fear-active populations in the retrosplenial cortex.

neuroscience↗

bioRxiv2023

MousiPLIER: A Mouse Pathway-Level Information Extractor Model

High throughput gene expression profiling is a powerful approach to generate hypotheses on the underlying causes of biological function and disease. Yet this approach is limited by its ability to infer underlying biological pathways and burden of testing tens of thousands of individual genes. Machine learning models that incorporate prior biological knowledge are necessary to extract meaningful pathways and generate rational hypothesis from the vast amount of gene expression data generated to date. We adopted an unsupervised machine learning method, Pathway-level information extractor (PLIER), to train the first mouse PLIER model on 190,111 mouse brain RNA-sequencing samples, the greatest amount of training data ever used by PLIER. mousiPLER converted gene expression data into a latent variables that align to known pathway or cell maker gene sets, substantially reducing data dimensionality and improving interpretability. To determine the utility of mousiPLIER, we applied it to a mouse brain aging study of microglia and astrocyte transcriptomic profiling. We found a specific set of latent variables that are significantly associated with aging, including one latent variable (LV41) corresponding to striatal signal. We next performed k-means clustering on the training data to identify studies that respond strongly to LV41, finding that the variable is relevant to striatum and aging across the scientific literature. Finally, we built a web server (http://mousiplier.greenelab.com/) for users to easily explore the learned latent variables. Taken together this study provides proof of concept that mousiPLIER can uncover meaningful biological processes in mouse transcriptomic studies. Significance statementAnalysis of RNA-sequencing data commonly generates differential expression of individual genes across conditions. However, genes are regulated in complex networks, not as individual entities. Machine learning models that incorporate prior biological information are a powerful tool to analyze human gene expression. However, such models are lacking for mouse despite the vast number of mouse RNA-seq datasets. We trained a mouse pathway-level information extractor model (mousiPLIER). The model reduced the data dimensionality from over 10,000 genes to 196 latent variables that map to prior pathway and cell marker gene sets. We demonstrated the utility of mousiPLIER by applying it to mouse brain aging data and developed a web server to facilitate the use of the model by the scientific community.

bioinformatics↗

bioRxiv2022

Cell-type-specific whole-genome landscape of ΔFOSB binding in nucleus accumbens after chronic cocaine exposure

The ability of neurons to respond to external stimuli involves adaptations of gene expression. The transcription factor, {Delta}FOSB, is important for the development of drug addiction, however, its gene targets have not been identified. Here we use CUT&RUN to map the genome-wide enrichment of {Delta}FOSB binding in the two major neuronal cell types of the nucleus accumbens, a key brain reward region, after cocaine exposure. The binding landscape shows that the majority of {Delta}FOSB peaks occur outside of promoter regions, including intergenic regions, and are surrounded by epigenetic marks indicative of active enhancers. BRG1, the core subunit of the SWI/SNF chromatin remodeling complex, overlaps with {Delta}FOSB peaks, consistent with earlier studies of {Delta}FOSBs interacting proteins. In addition, in silico analyses predict that {Delta}FOSB cooperatively regulates gene expression with homeobox and T-box transcription factors. These novel findings uncover key elements of {Delta}FOSBs molecular mechanisms in transcriptional regulation.

neuroscience↗

bioRxiv2022

Mapping PTBP splicing in human brain identifies targets for therapeutic splice switching including SYNGAP1

Alternative splicing of neuronal genes is controlled in part by the coordinated action of the polypyrimidine tract binding proteins (PTBP1 and PTBP2). While PTBP1 is ubiquitously expressed, PTBP2 is predominantly neuronal, controlling the expression of such targets as DLG4, which encodes PSD95, a protein important in synaptic function whose deficiency causes neurodevelopmental disorders. Here, we fully define the PTBP2 footprint in the human transcriptome using both human brain tissue and neurons derived from human induced pluripotent stem cells (iPSC-neurons). We identify direct PTBP2 binding sites and define PTBP2-dependent alternative splicing events, finding novel targets such as STXBP1 and SYNGAP1, which are synaptic genes also associated with neurodevelopmental disorders. The resultant PTBP2 binding and splicing maps were used to test if PTBP2 binding could be manipulated to increase gene expression in PTBP-targeted genes that cause disease when haploinsufficient. We find that PTBP2 binding to SYNGAP1 mRNA promotes alternative splicing and non-sense mediated decay. Antisense oligonucleotides that disrupt PTBP binding sites on SYNGAP1 redirect splicing and increase gene and protein expression. Collectively, our data provide a comprehensive view of PTBP2-dependent alternative splicing in human neurons and human cerebral cortex, guiding the development of novel therapeutic tools that may benefit a range of neurodevelopmental disorders.

molecular biology↗

bioRxiv2022

Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice.

BACKGROUNDCocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. HPTMs act combinatorically, yet few studies examine multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In the current study, we defined regulation of K4&K27 bivalency at Nr4a1 following cocaine treatment in male and female mice. The inclusion of female mice can shed light on the epidemiological relevance of sex to cocaine use disorder. METHODSMale and female mice were injected with saline or cocaine (i.p. 20mg/kg). We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). Pearsons correlation matrices quantified relationships within each brain region across treatment conditions for each sex. RESULTSWe defined K4&K27 bivalency at the Nr4a1 promoter in all three brain regions, in both sexes. In female STR, cocaine increased Nr4a1 mRNA, coupled to maintenance of Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and failed to increase Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC. CONCLUSIONThis study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice. Cocaine treatment in female mice increased Nr4a1 mRNA in STR, but there was no change in Nr4a1 H3K27me3 or K4&K27 promoter bivalency. Following cocaine treatment in male mice, Nr4a1 mRNA did not change in STR, HPC, or PFC, and Nr4a1 H3K27me3 and K4&K27 promoter bivalency increased in the STR.

neuroscience↗

bioRxiv2022

Cell-Type Specific Profiling of Histone Post-Translational Modifications in the Adult Mouse Striatum

Histone post-translational modifications (hPTMs) regulate gene expression via changes in chromatin accessibility and transcription factor recruitment. At a given locus, the coordinated enrichment of several distinct hPTMs regulate gene expression in response to external stimuli. However, neuronal hPTMs have been primarily characterized in bulk brain tissue and/or tissue pooled across subjects. This obscures both cell-type and individual variability, features essential to understand individual susceptibility to psychiatric disease. To address this limitation, we optimized a hybrid protocol, ICuRuS, to profile both activating and repressive hPTMs in neuronal subtypes from a single mouse. We report here profiling of striatal medium spiny neuron (MSN) subtypes, genetically defined by expression of Adenosine 2a Receptor (A2a) or Dopamine Receptor D1 (D1), which differentially regulate reward processing and pathophysiology. Using ICuRuS, we defined genome-wide, A2a- or D1-specific combinatorial hPTM profiles, and discovered regulatory epigenomic features at genes implicated in neurobiological function and disease.

neuroscience↗

bioRxiv2019

Set2-mediated alternative splicing of Srsf11 regulates cocaine reward behavior

Alternative splicing is a key mechanism for neuronal gene regulation, and is grossly altered in mouse brain reward regions following investigator-administered cocaine. It is well established that cocaine epigenetically regulates transcription, yet mechanism(s) by which cocaine-induced epigenetic modifications regulate alternative splicing is largely unexplored. Our group and others have previously identified the histone modification, H3K36me3, as a putative splicing regulator. However, it has not yet been possible to establish the direct causal relevance of this modification to alternative splicing in brain or any other context. We found that mouse cocaine self-administration caused widespread alternative splicing, concomitant with enrichment of H3K36me3 at splice junctions. Differentially spliced genes were enriched in the motif for splice factor, Srsf11, which was both differentially spliced and enriched in H3K36me3. Epigenetic editing led us to conclude that H3K36me3 functions directly in alternative splicing of Srsf11, and that Set2 mediated H3K36me3 bidirectionally regulates cocaine intake.

neuroscience↗