Biology subjects

Akil, H.

Publications and source records attributed to Akil, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Effects of panitumumab on the proteome of treated EGFRvIII glioblastoma cells and on their extracellular vesicles

Glioblastoma (GB) is an aggressive brain tumor for which reliable biomarkers of therapeutic response are still needed. Extracellular vesicles (EVs) can carry molecular components derived from their parent cells, thereby providing information on changes associated with the tumor and treatments. Among potential biomarkers, epidermal growth factor receptor variant III (EGFRvIII), is found in more than 40% of GB patients and is associated with aggressive tumor behavior and therapeutic resistance. EGFRvIII has also been detected on the surface of EVs, suggesting its potential value for monitoring tumor-associated molecular changes. This study investigated the effects of panitumumab, an anti-EGFR monoclonal antibody, on the proteomic profiles of EVs derived from EGFRvIII cells. U87 and U87-EGFRvIII cells and their derived EVs were characterized before and after treatment. EGFRvIII expression in cells and EVs was assessed by Western blotting and flow cytometry. Proteomic analyses were performed on cell lysates and EVs before and after treatment. Our results demonstrate that panitumumab significantly reduced surface EGFRvIII on EVs derived from U87-EGFRvIII cells, whereas no significant decrease was observed in cell lysates. This suggests that treatment may affect EGFRvIII trafficking or its incorporation into EVs. The proteomic analysis highlighted much more changes in EVs than in their parental cells after treatment, particularly in proteins associated with extracellular matrix organization and collagen. Together, these results demonstrate that panitumumab treatment is associated with changes in protein profile from EVs derived from EGFRvIII cells suggesting that the panitumumab treatment might have an impact on cells that could be reflected on EVs released by glioblastoma cells. In conclusion, our results suggest that EVs derived from EGFRvIII cells could serve as a useful circulating biomarker for assessing treatment efficacy and for preventing treatment escape.

cancer biology↗

bioRxiv2026

Deep in vivo brain metabolomics maps vulnerability-associated and cocaine-induced neurochemical states

Innate temperament affects vulnerability to substance use disorders (SUDs). Identifying the neurochemistry that differentiates temperaments, alongside the metabolic impact of drugs of abuse, can provide new insights into pathways to SUD and treatments. We show that heritable emotional temperaments associated with SUD vulnerability are encoded by distinct extracellular neurochemical states in the living brain. We apply untargeted metabolomics to microdialysis samples to define the chemical composition of the living brain metabolome with unprecedented depth. Using two phenotypes from a rodent model of diverging temperaments linked to SUDs, dialysate samples were collected before and after acute exposure to cocaine (15 mg/kg, i.p.). Metabolomic analysis revealed previously unknown basal differences in stress-response, bioenergetics, and amino acid neurotransmitters and their related pathways between the two phenotypes. Cocaine administration also had a profound impact on the metabolome, altering amino acid, purine, and arachidonic acid pathways along with cognition-related metabolites. Despite these broad metabolomic changes, cocaine administration narrowed several pre-existing differences between phenotypes, highlighting divergent responses across genetic lines. These findings demonstrate that in vivo metabolomics not only offers novel insights into the neurochemistry underlying temperament and drug response but also serves as framework to advance a systems-level understanding of other brain-related disorders.

neuroscience↗

bioRxiv2026

A Meta-Analysis of the Converging Effects of Different Classes of Antipsychotics on the Frontal Cortex Transcriptome in Laboratory Rodents and Non-Human Primates

BackgroundPsychotic illnesses are among the most debilitating classes of psychiatric disorders, requiring targeted and effective treatment strategies. Although antipsychotics are the primary pharmacological therapy for psychosis, their full range of effects remain unclear, including effects within the frontal cortex, a brain region linked structurally and functionally to psychotic disorders. MethodsTo examine the effects of antipsychotic treatment on the frontal cortex, we conducted a meta-analysis of publicly available rodent (rat, mice) transcriptional profiling datasets (microarray, RNA-Seq). Five datasets (GSE45229, GSE93918, GSE2547, GSE4031.1, GSE66275) were identified within the Gemma database using pre-specified search terms and inclusion/exclusion criteria (date: 7/7/2024), yielding differential expression results for eight drug vs. control comparisons (collective n=68). A random-effects meta-analysis model was fit to the log2 fold changes for each gene, and p-values adjusted for false discovery rate (FDR), with follow-up analyses exploring robustness, heterogeneity, and publication bias. To increase the power and generalizability of our findings, an exploratory meta-analysis was also run incorporating antipsychotic effects from both rodents and nonhuman primates (collective n=101), and compared to findings from individuals with schizophrenia. ResultsOur meta-analysis yielded stable estimates for 12,190 genes, identifying 63 genes that were differentially expressed following antipsychotic treatment ("DEGs", FDR<0.05). Differential expression included genes important for serotonergic and cholinergic signalling, and was enriched within pathways linked to oligodendrocyte development and myelination, physiological and cellular stress responses, and cardiovascular function. An exploratory meta-analysis combining rodent and nonhuman primate results confirmed these observations and yielded additional findings (117 DEGs total). Comparisons with human post-mortem findings suggested that some schizophrenia-related gene expression may instead reflect antipsychotic treatment. ConclusionFurther validation is necessary, but our findings suggest that antipsychotics may assist in the regulation of specific structural and functional changes within the frontal cortex linked to psychotic disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/734301v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1aaa2ecorg.highwire.dtl.DTLVardef@1ae6819org.highwire.dtl.DTLVardef@13454a2org.highwire.dtl.DTLVardef@a0877c_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIPsychosis is treated using two broad types of antipsychotic medication: first-generation (typical) and second-generation (atypical). C_LIO_LIUnderstanding the congruent effects of different types of antipsychotics on regions important for psychosis, such as the frontal cortex, can highlight essential mechanisms. C_LIO_LIA meta-analysis of public transcriptional profiling datasets identified genes and functional gene sets that are differentially expressed across antipsychotic categories. C_LI

neuroscience↗

bioRxiv2026

Differential acquisition of cocaine and heroin self-administration in a rat model of internalizing versus externalizing temperament

Substance Use Disorders (SUDs) constitute a major and rising public health concern. In addition, there is a growing appreciation that different classes of addictive substances are likely to lead to qualitatively different types of SUDs requiring differing treatment and relapse prevention strategies to be most effectively managed. Biological temperament, particularly on the internalizing - externalizing axis, is well established to influence addiction susceptibility. Externalizing behavior has long been understood to predispose individuals to addiction through novelty-seeking, sensation-seeking and impulsivity, while internalizing behavior provides an alternate pathway into addiction via increased occurrence of comorbid disorders (anxiety, depression). Here, we utilize a selectively bred rat model of internalizing vs externalizing temperament (bred High Responders, representing genetically mediated externalizing behavior and bred Low Responders, representing internalizing behavior) to examine differences in the acquisition of self-administration of the prototypical psychostimulant cocaine and the prototypical opioid heroin (diacetylmorphine). We found that, as predicted, cocaine and heroin drove different patterns of acquisition in the two different bred lines of rats. Further, this was influenced by temperament in complex ways. Notably, in females the "telescoping effect" for opioid addiction-like behavior was primarily specific to externalizing temperament. These findings highlight the impact and interaction of many factors, including drug class, temperament, and sex, on the acquisition of drug-taking behavior. Additionally, these findings indicate that sex differences in addiction vulnerability may be influenced in part by biological temperament.

animal behavior and cognition↗

bioRxiv2026

Significantly Improved Mouse and Rat Genome Annotation Using Sequence Read Archive RNA-seq Data

To detect currently unannotated genes with low expression levels with high sensitivity and accuracy, we developed a new exon->gene->transcript annotation pipeline that can identify previously undetected multi-exon transcripts using large volumes of RNA-Seq data. Our pipeline incorporates three new algorithms: 1) model-based spliced exon detection, 2) exon-to-gene assignment across multiple tissue/datasets through exon community discovery, and 3) ranking top transcripts by a stepwise minimum flow procedure. The design of our pipeline allowed us to leverage hundreds of Tbases of public RNA-seq data as input to improve mouse and rat genome annotation. Using this data, our pipeline identified close to 15K and 21K unannotated genes in GENCODE M37 and ENSEMBL 114 for mouse and rat, respectively. Each species also gained over 200K predicted transcripts containing at least one new exon, although most were transcripts from GENCODE/ENSEMBL annotated genes with newly assigned exons. To make our genome annotation available for common use, we have packaged this new annotation in standard file formats for the analysis of bulk and single cell RNA-seq data (GTF, 10X genome files). We have also provided two use examples which demonstrate the utility of our newly annotated genes in functional analyses, showing that their expression can be differentially regulated in relationship to cell type and selective breeding. Due to the efficiency provided by our pipeline, we expect that as new RNA-seq data become available in the coming years it will significantly benefit rat gene/transcript annotation, eventually enabling us to approach the target of complete gene and transcript annotation.

genomics↗

bioRxiv2026

Genetic Architecture of Addiction-Relevant Behaviors in Outbred Sprague-Dawley Rats Reveals Loci for Anxiety-Like and Nociceptive Traits

Studies have shown that substance use liability is associated with novelty seeking, anxiety-like behavior, and pain sensitivity. We examined whether common genetic variation in outbred Sprague-Dawley rats explained variation in behavioral measures from three assays with established links to substance use: locomotor response to a novel environment, elevated plus maze, and tail flick. We estimated single-nucleotide polymorphism heritability and performed genome-wide association analyses using permutation-derived significance thresholds (N=534-654 rats across traits). Heritability estimates ranged from 0.14-0.38 across eleven traits. Three independent loci were identified: chromosome 1 for elevated plus maze open-arm behavior (=0.05), chromosome 14 for elevated plus maze immobility (=0.10), and chromosome 17 for tail flick latency (=0.05). Candidate genes included Slc18a2, Gfra1, and Pdzd8 (chromosome 1); Rel and Bcl11a (chromosome 14); and Eci2 and Eci3 (chromosome 17). We compared these loci with our genome wide association study of a F2 intercross of selectively bred high- and low-responder rats, originally derived from Sprague-Dawleys, that model individual differences in externalizing and internalizing behavior. The current loci are distinct from the ones identified in the bred lines. This difference likely reflects selection history in the high- and low-responder F2s, which focused on facets of exploratory locomotion, while loci for anxiety and pain sensitivity traits were identified in the outbreds. This highlights the benefit of using both outbred and selectively bred rats to probe causal variants contributing to individual differences in substance use liability. The current outbred findings implicate monoaminergic signaling, transcriptional control, and lipid metabolism as testable mechanisms for addiction-relevant behaviors.

genetics↗

bioRxiv2025

A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence with Existing Human Data

BackgroundChronic stress is a major risk factor for psychiatric disorders, including anxiety, depression, and post-traumatic stress disorder. Chronic stress can cause structural alterations like grey matter atrophy in key emotion-related areas such as the prefrontal cortex (PFC). To identify biological pathways affected by chronic stress in the PFC, researchers have performed transcriptional profiling (RNA-sequencing, microarray) to measure gene expression in rodent models. However, transcriptional signatures in the PFC that are shared across different chronic stress paradigms and laboratories remain relatively unexplored. MethodsWe performed a meta-analysis of publicly available transcriptional profiling datasets within the Gemma database. We identified six datasets that characterized the effects of either chronic social defeat stress (CSDS) or chronic unpredictable mild stress (CUMS) on gene expression in the PFC in mice (n=117). We fit a random effects meta-analysis model to the chronic stress effect sizes (log(2) fold changes) for each transcript (n=21,379) measured in most datasets. We then compared our results with two other published chronic stress meta-analyses, as well as transcriptional signatures associated with psychiatric disorders. ResultsWe identified 133 genes that were consistently differentially expressed across chronic stress studies and paradigms (false discovery rate (FDR)<0.05). Fast Gene Set Enrichment Analysis (fGSEA) revealed 53 gene sets enriched with differential expression (FDR<0.05), dominated by glial and neurovascular markers (e.g., oligodendrocyte, astrocyte, endothelial/vascular) and stress-related signatures (e.g., major depressive disorder, hormonal responses). Immediate-early gene markers of neuronal activity (Fos, Junb, Arc, Dusp1) were consistently suppressed. Many of the identified effects resembled those seen in previous meta-analyses characterizing stress effects (CSDS, early life stress), despite minimal overlap in included samples. Moreover, some effects resembled previous observations from psychiatric disorders, including alcohol abuse disorder, major depressive disorder, bipolar disorder, and schizophrenia. ConclusionOur study demonstrates that chronic stress induces a robust, cross-paradigm PFC signature characterized by down-regulation of glia/myelin and vascular pathways and suppression of immediate-early gene activity, highlighting cellular processes linking chronic stress exposure, PFC dysfunction, and psychiatric disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/683091v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1062c5eorg.highwire.dtl.DTLVardef@4ae148org.highwire.dtl.DTLVardef@c747corg.highwire.dtl.DTLVardef@1b3a713_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIChronic stress is linked to many human psychiatric disorders involving the prefrontal cortex (PFC). C_LIO_LIMeta-analysis showed that stressed mice had less gene expression for glia and neural activity in the PFC. C_LIO_LIPFC gene expression in chronically stressed mice mirrors patterns seen in psychiatric patients. C_LI Plain Language SummaryChronic stress has been shown to have lasting effects on the brain, contributing to cognitive impairments and the risk of psychiatric disorders such as anxiety, depression, and post-traumatic stress disorder. The prefrontal cortex, a brain region that is important for behavioral and attentional control, is sensitive to chronic stress. We combined information from six public mouse datasets to identify consistent effects of chronic stress on gene expression (mRNA) in the prefrontal cortex. In these studies, mice that had experienced chronic stress showed a decreased amount of mRNA related to a variety of non-neuronal support cells (glia) and blood vessels, and general neural activity. The mouse chronic stress signature overlapped with gene-activity patterns reported in human psychiatric conditions, suggesting a biological bridge between chronic stress and the onset of psychopathology.

neuroscience↗

bioRxiv2025

Effect of Chronic Stress on Whole Blood Transcriptome: A Meta-Analysis of Publicly Available Datasets from Rodent Models

BackgroundChronic stress increases risk for neuropsychiatric disorders in humans. By modeling stress-induced changes in animals, we may improve diagnosis or treatment of these disorders. Successful translation benefits from studies with sufficient statistical power and outcome measurements that can be directly compared across species. We performed a meta-analysis to examine the impact of chronic stress on the whole blood transcriptome. MethodsDatasets were systematically identified in Gemma, a database of reprocessed public transcriptional profiling studies; datasets GSE68076, GSE72262, and GSE84185 met inclusion/exclusion parameters. Each study exposed eight-week old mice to chronic stress (5-10 days social defeat stress or 6-8 weeks chronic mild stress). The final sample size was n=92 (n=45 Non-Stress/n=47 Stress). Stress-related differential expression in each dataset was quantified using the Limma pipeline followed by empirical Bayes moderation. For the 9,219 genes represented in all three datasets, we ran a meta-analysis of Log(2) Fold Changes using a random effects model and corrected for false discovery rate (FDR). Functional patterns were assessed with fast Gene Set Enrichment Analysis. Cell type specific enrichment for each of the differentially expressed genes was further explored using a public 10x genomics scRNA-Seq dataset from mouse peripheral blood mononuclear cells. ResultsFindings included 23 downregulated and 16 upregulated transcripts in stress-exposed mice (FDR<0.05). Results indicated a down-regulation in gene sets related to B cells, immune response, DNA and chromatin regulation, ribosomal activity, translation, and catabolic cellular processes. Upregulated gene sets related to erythrocytes and oxygen binding. ConclusionOur results provide molecular insight into stress-related immune dysregulation and add weight to the hypothesis that environmental stress escalates cellular aging, supporting the use of blood transcriptome as a bridge between human and rodent models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/657043v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@161fc2eorg.highwire.dtl.DTLVardef@1f358b9org.highwire.dtl.DTLVardef@145ef33org.highwire.dtl.DTLVardef@5b1169_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsSuccessful translational research benefits from studies with outcome measurements that can be directly compared across species and sufficient statistical power. The present report is a meta-analysis of three mouse experiments examining the impact of chronic stress on the whole blood transcriptome. Our results provide insight into stress-related immune dysregulation and add weight to the hypothesis that environmental stress escalates cellular aging. These findings illustrate the utility of the blood transcriptome as a bridge between human and rodent models.

genomics↗

bioRxiv2025

Short Report: A Meta-Analysis of the Effects of Sleep Deprivation on the Cortical Transcriptome in Animal Models

Sleep deprivation (SD) causes large disturbances in mood and cognition. The molecular basis for these effects can be explored using transcriptional profiling to quantify brain gene expression. In this report, we used a meta-analysis of public transcriptional profiling data to discover SD effects on gene expression that are consistent across studies and paradigms. To conduct the meta-analysis, we used pre-specified search terms related to rodent SD paradigms to identify relevant studies within Gemma, a database containing >19,000 re-analyzed microarray and RNA-Seq datasets. Eight studies met our systematic inclusion/exclusion criteria. These studies characterized the effect of 18 SD interventions on gene expression in the mouse cerebral cortex (collective n=293). For each gene with sufficient data (n=16,290), we fit a random effects meta-analysis model to the SD effect sizes (log(2) fold changes). Our meta-analysis revealed 182 differentially expressed genes in response to SD (false discovery rate: FDR<0.05), most of which (115/182) showed similar effects (FDR<0.05) in an independent large dataset (GSE114845: n=86 RNA-Seq samples from n=222 mice). Gene-set enrichment analysis revealed down-regulation in pathways related to stress response (e.g., glucocorticoid receptor Nr3c1), vasculature, growth and development, and upregulation related to stress, inflammation, and neuropeptide signalling. Exploratory analyses suggested that recovery sleep (included in six contrasts: range: 1-18 hrs), could reverse the impact of SD on gene expression. Our meta-analysis provides a useful reference database illustrating the diverse molecular impact of SD on the rodent cerebral cortex. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/648791v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@52984dorg.highwire.dtl.DTLVardef@8d1174org.highwire.dtl.DTLVardef@174ed85org.highwire.dtl.DTLVardef@195e8bf_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

neuroscience↗

bioRxiv2025

The Effects of Antidepressants on the Hippocampus: A Meta-Analysis of Public Transcriptional Profiling Data

Depression can be treated with traditional pharmaceuticals targeting monoaminergic function, non-traditional drug classes and neuromodulatory interventions. To identify mechanisms of action shared across clinically-effective antidepressant treatment categories, we performed two systematic meta-analyses of public transcriptional profiling data from adult laboratory rodents (rats, mice). The outcome variable was gene expression, measured by microarray or RNA-Seq from bulk-dissected tissue from two depression-related brain regions (hippocampus, cortex). Relevant datasets were identified in the Gemma database of curated, reprocessed transcriptional profiling data using predefined search terms and inclusion/exclusion criteria (hippocampus: 6-24-2024, cortex: 7-10-2024). Differential expression results were extracted for all genes, minimizing bias. For each gene, a random effects meta-analysis model was fit to antidepressant vs. control effect sizes (Log2 Fold Changes) from each study for each brain region, with follow-up analyses exploring sources of effect heterogeneity. For the hippocampus, 15 relevant studies were identified, containing 22 antidepressant vs. control group comparisons (collective n=313 samples), with approximately half representing traditional versus non-traditional antidepressants. Of 16,439 analyzed genes, 58 were consistently differentially expressed (False Discovery Rate (FDR)<0.05) following treatment. Antidepressant effects were enriched in the dentate gyrus and in gene sets related to stress regulation, brain growth and plasticity, vasculature and glia, and immune function. Comparisons with single nucleus RNA-Seq confirmed effects on specific hippocampal cell types, including potential rejuvenation of dentate granule neurons. For the cortex, 13 studies were identified, containing 16 antidepressant vs. control group comparisons (collective n=233 samples). Of 15,583 analyzed genes, only one was consistently differentially expressed (FDR<0.05: Atp6v1b2), but overall expression patterns moderately resembled the hippocampus. These genes and pathways showing consistent differential expression across treatment categories may be promising targets for novel therapies. Future work should explore relevance to human clinical populations and potential heterogeneity introduced by sex and subregion. Key PointsO_LIDepression can be treated with traditional antidepressants targeting monoaminergic function, as well as other drug classes and non-pharmaceutical interventions. C_LIO_LIUnderstanding the congruent effects of different types of antidepressant treatments on sensitive brain regions, such as the hippocampus and cortex, can highlight essential mechanisms of action. C_LIO_LIA meta-analysis of public transcriptional profiling datasets identified genes and functional gene sets that are differentially expressed across antidepressant categories. C_LI Plain Language SummaryMajor depressive disorder is characterized by persistent depressed mood and loss of interest and pleasure in life. Worldwide, an estimated 5% of adults suffer from depression, making it a leading cause of disability. The current standard of care for depressed individuals includes psychotherapy and antidepressant medications that enhance signaling by monoamine neurotransmitters, such as serotonin and norepinephrine. Other treatments include non-traditional antidepressants that function via alternative, often unknown, mechanisms. To identify mechanisms of action shared across different categories of antidepressants, we performed a meta-analysis using public datasets to characterize changes in gene expression (mRNA) following treatment with both traditional and non-traditional antidepressants. We focused on the hippocampus and cortex, which are two brain regions that are sensitive to both depression and antidepressant usage. We found 59 genes that had consistently higher or lower levels of expression (mRNA) across antidepressant categories. The functions associated with these genes were diverse, including regulation of stress response, the immune system, brain growth and adaptability. These genes are worth investigating further as potential linchpins for antidepressant efficacy or as targets for novel therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/648805v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@14538e3org.highwire.dtl.DTLVardef@199c5e3org.highwire.dtl.DTLVardef@8ed8a6org.highwire.dtl.DTLVardef@31b1f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

A meta-analysis of the effects of early life stress on the prefrontal cortex transcriptome suggests long-term effects on myelin

BackgroundEarly life stress (ELS) refers to exposure to negative childhood experiences, such as neglect, disaster, and physical, mental, or emotional abuse. ELS can permanently alter the brain, leading to cognitive impairment, increased sensitivity to future stressors, and mental health risks. The prefrontal cortex (PFC) is a key brain region implicated in the effects of ELS. MethodsTo better understand the effects of ELS on the PFC, we ran a meta-analysis of publicly available transcriptional profiling datasets. We identified five datasets (GSE89692, GSE116416, GSE14720, GSE153043, GSE124387) that characterized the long-term effects of multi-day postnatal ELS paradigms (maternal separation, limited nesting/bedding) in male and female laboratory rodents (rats, mice). The outcome variable was gene expression in the PFC later in adulthood as measured by microarray or RNA-Seq. To conduct the meta-analysis, preprocessed gene expression data were extracted from the Gemma database. Following quality control, the final sample size was n=89: n=42 controls & n=47 ELS: GSE116416 n=23 (no outliers); GSE116416 n=44 (2 outliers); GSE14720 n=7 (no outliers); GSE153043 n=9 (1 outlier), and GSE124387 n=6 (no outliers). Differential expression was calculated using the limma pipeline followed by an empirical Bayes correction. For each gene, a random effects meta-analysis model was then fit to the ELS vs. Control effect sizes (Log2 Fold Changes) from each study. ResultsOur meta-analysis yielded stable estimates for 11,885 genes, identifying five genes with differential expression following ELS (false discovery rate< 0.05): transforming growth factor alpha (Tgfa), IQ motif containing GTPase activating protein 3 (Iqgap3), collagen, type XI, alpha 1 (Col11a1), claudin 11 (Cldn11) and myelin associated glycoprotein (Mag), all of which were downregulated. Broadly, gene sets associated with oligodendrocyte differentiation, myelination, and brain development were downregulated following ELS. In contrast, genes previously shown to be upregulated in Major Depressive Disorder patients were upregulated following ELS. ConclusionThese findings suggest that ELS during critical periods of development may produce long-term effects on the efficiency of transmission in the PFC and drive changes in gene expression similar to those underlying depression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/624315v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1619926org.highwire.dtl.DTLVardef@8da510org.highwire.dtl.DTLVardef@14feffcorg.highwire.dtl.DTLVardef@114aae3_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIEarly life stress (ELS) can have long-term effects on the prefrontal cortex (PFC) and its related cognitive and emotional functions. C_LIO_LITo elucidate these long-term effects, we conducted a meta-analysis of five publicly available PFC transcriptional profiling datasets from adult rodents that had previously experienced ELS. C_LIO_LIThis meta-analysis revealed a consistent downregulation of myelin-related genes in the PFC following ELS, and an upregulation of genes related to Major Depressive Disorder. C_LI Plain Language SummaryEarly life stress refers to exposure to negative childhood experiences, such as neglect, disaster, and physical, mental, or emotional abuse. Early life stress can permanently alter the brain, including the prefrontal cortex, which can lead to cognitive and emotional dysfunction that lasts into adulthood. We performed a meta-analysis using five public datasets to identify consistent long-term effects of early life stress on gene expression (mRNA) in the prefrontal cortex of adult rodents. In these studies, rodents that had experienced early life stress consistently showed a decreased amount of mRNA for genes related to myelin. Myelin is the fatty layer that insulates the axons of neurons, allowing them to transmit electrical signals more efficiently. These gene expression changes may suggest long-term effects of early life stress on the efficiency of prefrontal neurotransmission, disrupting cognitive and emotional processing.

neuroscience↗

bioRxiv2024

Resource: A Curated Database of Brain-Related Functional Gene Sets (Brain.GMT)

O_LITranscriptional profiling has become a common tool for investigating the nervous system. During analysis, differential expression results are often compared to functional ontology databases, which contain curated gene sets representing well-studied pathways. This dependence can cause neuroscience studies to be interpreted in terms of functional pathways documented in better studied tissues (e.g., liver) and topics (e.g., cancer), and systematically emphasizes well-studied genes, leaving other findings in the obscurity of the brain "ignorome". C_LIO_LITo address this issue, we compiled a curated database of 918 gene sets related to nervous system function, tissue, and cell types ("Brain.GMT") that can be used within common analysis pipelines (GSEA, limma, edgeR) to interpret results from three species (rat, mouse, human). Brain.GMT includes brain-related gene sets curated from the Molecular Signatures Database (MSigDB) and extracted from public databases (GeneWeaver, Gemma, DropViz, BrainInABlender, HippoSeq) and published studies containing differential expression results. C_LIO_LIAlthough Brain.GMT is still undergoing development and currently only represents a fraction of available brain gene sets, "brain ignorome" genes are already better represented than in traditional Gene Ontology databases. Moreover, Brain.GMT substantially improves the quantity and quality of gene sets identified as enriched with differential expression in neuroscience studies, enhancing interpretation. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/588301v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@d8a5beorg.highwire.dtl.DTLVardef@1697a1aorg.highwire.dtl.DTLVardef@1cf4cf8org.highwire.dtl.DTLVardef@c634dd_HPS_FORMAT_FIGEXP M_FIG C_FIG Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@b8ac07org.highwire.dtl.DTLVardef@2628f8org.highwire.dtl.DTLVardef@14bb803org.highwire.dtl.DTLVardef@1ddbfborg.highwire.dtl.DTLVardef@5567e8_HPS_FORMAT_FIGEXP M_TBL C_TBL

neuroscience↗

bioRxiv2024

Cell-Type Specific Reductions in Interneuron Gene Expression within Subregions of the Anterior and Posterior Cingulate Gyrus of Schizophrenia and Bipolar Disorder Subjects

Schizophrenia (SZ) and bipolar disorder (BP) patients share overlapping and distinct neurocognitive deficits. Neuroimaging of these patients and postmortem gene expression analyses suggest that compromised cingulate gyrus GABA-ergic interneurons may contribute to cognitive impairments in SZ and BP. Therefore, we investigated potential gene expression signatures for SZ and BP using interneuron cell-type specific markers including glutamic acid decarboxylase (GAD67), parvalbumin (PV), somatostatin (SST), and vasoactive intestinal peptide (VIP) within cingulate Brodmanns areas (BA). We report reduced GAD67 mRNA in anterior midcingulate cortex (aMCC) of SZ and BP subjects with BA24c being most dysregulated across disorders, demonstrating reduced PV (SZ), SST (BP), and VIP mRNA (SZ and BP). Dorsal posterior cingulate (dPCC) displayed decreased SST (BP) whereas retrosplenial cortex (RSC) showed reduced PV (SZ and BP) and SST mRNA (BP). Our results show shared and unique transcription signatures of two disorders in specific cingulate gyrus regions and cell types. SZ and BP show a similar profile of aMCC gene expression reductions suggesting subregional dysregulation within areas associated with error/action monitoring and the saliency network. In dPCC/RSC, transcriptional changes are associated with disease-specific gene/subregion signatures, possibly underlying differential effects on allocation of attentional resources and visuospatial memory processing unique to each disorder.

neuroscience↗

bioRxiv2023

Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs

Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.

genomics↗

bioRxiv2023

Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype

Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the "internalizing" bred Low Responder (bLR) line versus the "externalizing" bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Male bLR and bHR rats were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused rats to display more social interaction, as well as nominally less social avoidance, less submission during defeat, and resilience to the effects of social stress on corticosterone, in a manner that seemed more notable in bLRs. For bHRs, enrichment also caused greater aggression during a neutral social encounter and nominally during defeat, and decreased anxiety-like behavior. To explore the neurobiology underlying the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. Our findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.

neuroscience↗

bioRxiv2023

Extensive profiling of transcription factors in postmortem brains defines genomic occupancy in disease-relevant cell types and links TF activities to neuropsychiatric disorders

Transcription factors (TFs) orchestrate gene expression programs crucial for cell physiology, but our knowledge of their function in the brain is limited. Using bulk tissues and sorted nuclei from multiple human post-mortem brain regions, we generated a multi-omic resource (1121 total experiments) that includes binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of regions of high TF occupancy. Further, we find that predictive TF binding models demonstrate a bias for these high occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Several TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. These data are a powerful resource for future studies seeking to understand the role of TFs in epigenetic regulation in the human brain.

genomics↗

bioRxiv2023

Inhibition of dopamine neurons prevents incentive value encoding of a reward cue:With revelations from deep phenotyping

The survival of an organism is dependent on their ability to respond to cues in the environment. Such cues can attain control over behavior as a function of the value ascribed to them. Some individuals have an inherent tendency to attribute reward-paired cues with incentive motivational value, or incentive salience. For these individuals, termed sign-trackers, a discrete cue that precedes reward delivery becomes attractive and desirable in its own right. Prior work suggests that the behavior of sign-trackers is dopamine-dependent, and cue-elicited dopamine in the nucleus accumbens is believed to encode the incentive value of reward cues. Here we exploited the temporal resolution of optogenetics to determine whether selective inhibition of ventral tegmental area (VTA) dopamine neurons during cue presentation attenuates the propensity to sign-track. Using male tyrosine hydroxylase (TH)-Cre Long Evans rats it was found that, under baseline conditions, [~]84% of TH-Cre rats tend to sign-track. Laser-induced inhibition of VTA dopamine neurons during cue presentation prevented the development of sign-tracking behavior, without affecting goal-tracking behavior. When laser inhibition was terminated, these same rats developed a sign-tracking response. Video analysis using DeepLabCut revealed that, relative to rats that received laser inhibition, rats in the control group spent more time near the location of the reward cue even when it was not present and were more likely to orient towards and approach the cue during its presentation. These findings demonstrate that cue-elicited dopamine release is critical for the attribution of incentive salience to reward cues. Significance StatementActivity of dopamine neurons in the ventral tegmental area (VTA) during cue presentation is necessary for the development of a sign-tracking, but not a goal-tracking, conditioned response in a Pavlovian task. We capitalized on the temporal precision of optogenetics to pair cue presentation with inhibition of VTA dopamine neurons. A detailed behavioral analysis with DeepLabCut revealed that cue-directed behaviors do not emerge without VTA dopamine. Importantly, however, when optogenetic inhibition is lifted, cue-directed behaviors increase, and a sign-tracking response develops. These findings confirm the necessity of VTA dopamine during cue presentation to encode the incentive value of reward cues.

neuroscience↗

bioRxiv2023

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-- mRatBN7.2--corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined [~]20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

genomics↗