Biology subjects

McClung, C. A.

Publications and source records attributed to McClung, C. A..

14 recordsLinked to original sources

bioRxiv2026

Diurnal Variations in the Cholinergic System of the Nucleus Accumbens

The nucleus accumbens (NAc) plays a critical role in reward-related behaviors, which exhibit diurnal variations. Cholinergic interneurons (CINs) are the primary source of acetylcholine within the NAc and regulate local dopamine (DA) signaling through nicotinic acetylcholine receptors (nAChRs). Although there are diurnal variations in NAc dynamics, little is known about whether CIN activity and nicotinic signaling also vary across the light/dark cycle. Here, we aimed to determine diurnal variations in the NAc cholinergic system using ex vivo fast-scan cyclic voltammetry and cell-attached electrophysiological recordings in male rodents. We examined time-of-day-dependent differences in nAChR-mediated modulation of DA release, spontaneous CIN firing frequency, and firing patterns. We found that spontaneous CIN firing varied across the light/dark cycle, with increased activity during the dark cycle. Additionally, bath application of nicotine (NIC), mecamylamine (MEC), and dihydro-{beta}-erythroidine (DH{beta}E) reduced CIN firing frequency during the dark cycle, with only MEC decreasing firing frequency in the light cycle. NIC and MEC also altered CIN firing patterns during the dark cycle, whereas DH{beta}E primarily affected firing frequency. Together, these findings demonstrate diurnal variations in NAc CIN activity and reveal time-of-day-dependent differences in the effects of nAChR modulation on spontaneous firing. These results suggest that nicotinic signaling may contribute to diurnal regulation of NAc cholinergic activity, providing insight into mechanisms underlying time-of-day-dependent changes in reward circuitry.

neuroscience↗

bioRxiv2026

Gene-specific exponent-corrected normalization for library size in bulk RNA-seq

Correcting for library size is an essential step in bulk RNA-seq analyses, as differences in sequencing depth across samples can obscure biological signal with technical noise. While numerous normalization methods and model-based strategies have been proposed, we demonstrate here that library size-normalized counts and differential expression results obtained from such widely adopted approaches often remain strongly correlated with library size in large-scale RNA-seq experiments. Through a systematic analysis of over 100 publicly available GEO and TCGA RNA-seq datasets with raw count data, we show that library size association is observed for a substantial proportion of genes even after state-of-the-art library size correction approaches recommended by leading normalization tools. To address this issue, we propose gecco, a gene-specific exponent-corrected normalization method for RNA-seq counts that incorporates library size directly into the statistical framework via a gene-specific correction term, rather than applying a uniform adjustment factor across all genes. This formulation generalizes existing normalization approaches and yields normalized counts that are free of residual library size effects. Using both simulation studies and real large-scale RNA-seq datasets, we show that our method mitigates library size bias while preserving biological signal across a range of parameter settings. We further demonstrate that our approach leads to higher detection accuracy and more biologically meaningful pathway enrichment results in downstream differential expression and rhythmicity analyses without compromising false discovery rate control. Our method is implemented in R and is fully compatible with the widely used differential expression analysis methods DESeq2 and edgeR.

bioinformatics↗

bioRxiv2026

Prenatal circadian rhythm disruption induces sex-specific substance use and mood-related phenotypes in mice

20% of Americans are at risk for environmental circadian rhythm disruptions (CRD) due to shift work, leading to substantial negative health outcomes. However, females are especially affected with greater vulnerability for substance use (SU) and adverse outcomes associated with pregnancy, including for offspring at birth and later in life. In mice, prenatal CRD (pCRD) recapitulates these risks, but it is unknown whether pCRD affects SU in mature offspring. To investigate this, C57BL/6J dams were disrupted by reversing the light/dark cycle during gestation. Following pCRD, reward- (cocaine conditioned place preference, intravenous self-administration) and mood-related behaviors (open field, elevated plus maze, light/dark box, forced swim) were measured in adult offspring. Adult female offspring of dams exposed to CRD developed an anhedonic-like phenotype with decreased food self-administration, cocaine intake and reinforcing properties of cocaine. Opposingly, pCRD male offspring showed a SU-like phenotype with increased cocaine preference, higher order food self-administration and cocaine reinforcement. Interestingly, these divergent behavioral outcomes were not specific to reward. While female pCRD mice showed increased anxiety-like behavior, pCRD males showed decreased anxiety/increased risk-taking behavior, as well as decreased immobility in the forced swim test. Rhythms in corticosterone were also sex-specifically affected by pCRD. These results suggest that pCRD may predispose individuals to distinct psychiatric disorders based on sex with mood disorders developing in females and SU disorders developing in males. By better understanding how disrupted rhythms during pregnancy affect behavior in adulthood, we can develop novel therapeutic approaches for SU and mood disorders in adults.

neuroscience↗

bioRxiv2026

Identification of Genomic Loci Associated with Cellular Rhythms in Diversity Outbred Mice

Inter-individual variation in human molecular and behavioral circadian rhythms motivates genetic dissection in model systems with human-like diversity. We quantified cellular clock phenotypes from primary skin fibroblasts of several hundred Diversity Outbred (DO) mice-each carrying a unique mosaic of eight founder genomes-by longitudinal bioluminescence recordings of a Bmal1-luciferase reporter (LumiCycle). Canonical rhythm parameters (period, phase, amplitude, damping) were extracted and exhibited broad variability (heritability {approx}13-35%), exceeding the ranges of founder strains. We performed genome-wide QTL mapping with R/qtl2 (linear mixed models with sex and experimental group covariates, kinship control, permutation-based significance, 1.5-LOD support intervals). A suggestive QTL for amplitude localized to chromosome 12 (LOD 6.9; [~]7.5-12.0 Mb), with founder effects indicating higher amplitude for C57BL/6J and lower for PWK/PhJ. Among 21 protein-coding genes in this interval, Apob (apolipoprotein B), a clock-regulated determinant of lipoprotein assembly, emerged as a strong candidate for amplitude control. A phase QTL mapped to chromosome 1 (support interval [~]1.36 Mb) with divergent founder effects (C57BL/6J, NOD/ShiLtJ, WSB/EiJ: delayed; PWK/PhJ, CAST/EiJ: advanced) and prioritized candidates including Epha4 (an Eph receptor tyrosine kinase implicated in photic entrainment) and Acsl3. Integrative analysis in GeneWeaver connected QTL gene sets to prior loci for voluntary alcohol consumption and circadian period on proximal chromosome 12, and highlighted overlaps with GWAS signals for adolescent idiopathic scoliosis and schizophrenia, suggesting shared pathways between circadian regulation, metabolism, and neurobehavioral traits. Together, these findings define reproducible genomic loci for cellular clock phenotypes in a highly recombinant population, nominate tractable candidate genes (Apob, Epha4/Acsl3) for mechanistic follow-up, and illustrate how high-diversity mouse genetics bridges cellular circadian variation with complex disease biology.

genetics↗

bioRxiv2026

Unraveling Tissue-Specific Molecular Signatures and Convergent Pathway Enrichments in Suicidal Behavior

Suicide is a leading cause of death worldwide, yet the biological mechanisms underlying suicide remain poorly understood. A clearer understanding at the molecular level is essential for developing objective biomarkers and targeted interventions. In this study, we used transcriptomic profiling to investigate gene expression patterns associated with suicidal thoughts and behaviors across peripheral blood (n=264) and postmortem brain tissue from two prefrontal regions (dorsolateral prefrontal cortex, DLPFC; subgenual anterior cingulate cortex, sgACC) of individuals with and without psychiatric illness (n=249). Peripheral analyses revealed broad transcriptional changes associated with suicidal thoughts and behaviors, marked by dysregulated immune-related and inflammatory processes. Longitudinal modeling further revealed gene co-expression modules that predicted future suicide attempts over a 12-month follow-up, highlighting processes related to apoptosis, mitochondrial function, and immune regulation. By contrast, transcriptomic analyses of postmortem tissue derived from the DLPFC and sgACC revealed largely suppressed neuroimmune activity. Gene co-expression analyses in the brain identified suicide-associated modules enriched for synaptic plasticity, oxidative stress, and neuroimmune function, some of which displayed regional specificity. Cross-tissue comparison showed minimal gene-level overlap between brain and blood, although shared pathway-level themes emerged in immune, sensory, and cellular stress processes. Taken together, these findings suggest that suicide is associated with distinct but functionally convergent transcriptional alterations across brain and blood. By integrating tissue-specific and systems-level molecular signatures, this work provides insight into the biological architecture of suicide and lays the groundwork for developing novel biomarkers and therapeutic targets to improve prevention and treatment outcomes.

neuroscience↗

bioRxiv2026

Zwitterionic polymer coating enabled chronic dopamine sensing and electrophysiology recording in free-moving mice

The brains complex network relies on both electrical and chemical signaling to support its physiological and cognitive functions. To fully understand neural circuit dynamics and their dysfunctions, it is crucial to simultaneously detect neurotransmitters and modulators alongside electrophysiological signals. The striatal dopamine circuits are integral to neurological processes such as movement, reward, learning, and circadian rhythm regulation, making it highly desirable to monitor both neural activity and dopamine (DA) levels in freely behaving animals. One promising approach involves the implantation of multimodal microelectrode arrays (MEAs). However, chronic electrochemical sensing of DA in freely moving animals faces significant challenges, including biofouling of sensing electrodes and the instability of Ag/AgCl reference electrodes. In this study, we developed two complementary strategies--surface grafting and photo crosslinking--to coat the MEA and implanted Ag/AgCl reference electrodes, respectively, with zwitterionic poly(sulfobetaine methacrylate) (PSB). The surface-grafted thin PSB coating effectively inhibits protein fouling and inflammatory responses to the MEA, while the PSB hydrogel protects the Ag/AgCl electrodes from delamination in vivo, ensuring a stable reference potential. By coating both the Ag/AgCl reference electrodes and flexible polyimide MEAs with PSB and PEDOT/CNT, we achieved stable DA detection and electrophysiological recordings in freely moving mice over a four-week period. Weekly electrochemical impedance spectroscopy confirmed the long-term stability of the implanted electrodes. Our method enables multidimensional analysis of behavioral patterns, electrophysiological activity, and DA dynamics, providing a comprehensive approach for neuroscience research. This work advances neurochemical and electrophysiological methodologies by offering reliable tools for longitudinal investigations of brain function in freely behaving animals.

bioengineering↗

bioRxiv2024

Comparative transcriptomic rhythms in the mouse and human prefrontal cortex

Alterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents. Here, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC). We find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes. Together, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.

neuroscience↗

bioRxiv2024

Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex

Previous studies have shown that there are rhythms in gene expression in the mouse prefrontal cortex (PFC); however, the contribution of different cell types and potential variation by sex has not yet been determined. Of particular interest are excitatory pyramidal cells and inhibitory parvalbumin (PV) interneurons, as interactions between these cell types are essential for regulating the excitation/inhibition balance and controlling many of the cognitive functions regulated by the PFC. In this study, we identify cell-type specific rhythms in the translatome of PV and pyramidal cells in the mouse PFC and assess diurnal rhythms in PV cell electrophysiological properties. We find that while core molecular clock genes are conserved and synchronized between cell types, pyramidal cells have nearly twice as many rhythmic transcripts as PV cells (35% vs. 18%). Rhythmic transcripts in pyramidal cells also show a high degree of overlap between sexes, both in terms of which transcripts are rhythmic and in the biological processes associated with them. Conversely, in PV cells, rhythmic transcripts from males and females are largely distinct. Moreover, we find sex-specific effects of phase on action potential properties in PV cells that are eliminated by environmental circadian disruption. Together, this study demonstrates that rhythms in gene expression and electrophysiological properties in the mouse PFC vary by both cell type and sex. Moreover, the biological processes associated with these rhythmic transcripts may provide insight into the unique functions of rhythms in these cells, as well as their selective vulnerabilities to circadian disruption. Significance statementThis is the first study to examine translatomic rhythms in the mouse PFC with cell-type specificity. We find that the core molecular clock cycles in phase across cell types, indicating that previously described daily oscillations in the cortical excitation/inhibition balance are not the consequence of a phase offset between PV and pyramidal cells. Nevertheless, rhythmic transcripts and their associated biological processes differ by both sex and cell type, suggesting that molecular rhythms may play a unique role in different cell types and between sexes. Therefore, our results, such as the enrichment of transcripts associated with mitochondrial function in PV cells from males, point towards possible cell and sex-specific mechanisms that could contribute to psychiatric and cognitive diseases upon rhythm disruption.

neuroscience↗

bioRxiv2024

A widespread electrical brain network encodes anxiety in health and depressive states

In rodents, anxiety is characterized by heightened vigilance during low-threat and uncertain situations. Though activity in the frontal cortex and limbic system is fundamental to supporting this internal state, the underlying network architecture that integrates activity across brain regions to encode anxiety across animals and paradigms remains unclear. Here, we utilize parallel electrical recordings in freely behaving mice, multiple translational paradigms known to induce anxiety, and machine learning to discover a multi-region network that encodes the anxious brain state. The network is composed of circuits widely implicated in anxiety behavior, it generalizes across many behavioral contexts that induce anxiety, and it fails to encode multiple behavioral contexts that do not. Strikingly, the activity of this network is also principally altered in two mouse models of depression. Thus, we establish a network-level process whereby the brain encodes anxiety in health and disease.

neuroscience↗

bioRxiv2022

The magnitude of sex differences in host-microbe interactions are time-of-day dependent

Circadian rhythms dynamically regulate sex differences in metabolism and immunity, and circadian disruption increases the risk of metabolic disorders. We investigated the role of sex-specific microbial circadian rhythms in host metabolism using germ-free and conventionalized female and male mice, dietary manipulations, coupled with a systems biology approach. Sex differences in circadian rhythms of genes involved in immunity and metabolism are dependent on oscillations in the microbiota, microbial metabolic functions, and microbial metabolites. Further, dietary factors modify the magnitude of sex differences in host-microbe circadian dynamics. We show that consuming an obesogenic high-fat, low-fiber diet produced sex-specific changes in circadian rhythms in microbiota, metabolites, and host gene expression, which were linked to sex differences in the severity of metabolic dysfunction. These results reveal that microbial circadian rhythms contribute to sex differences in metabolism, emphasizing the need to consider sex as a biological variable in research on microbial contributions to metabolic dysfunction. HIGHLIGHTSO_LIMicrobial circadian rhythms differ by sex. C_LIO_LISex-specific rhythms in host transcriptional networks are microbiome-dependent. C_LIO_LIDiet-induced obesity entrains new sex-specific rhythms in microbiome and host genes. C_LIO_LITiming of data collection influences magnitude of sex differences. C_LI

systems biology↗

bioRxiv2022

The ultradian transcriptome of the human prefrontal cortex and abnormalities in schizophrenia

Twelve-hour (12 h) ultradian rhythms are a well-known phenomenon in coastal marine organisms. While 12 h cycles are observed in human behavior and physiology, no study has measured 12 h rhythms in the human brain. Here we identify 12 h rhythms in transcripts which either peak at sleep/wake transitions (~9 AM/PM) or static times (~3 PM/AM) in the dorsolateral prefrontal cortex, a region involved in cognition. Subjects with schizophrenia lose 12 h rhythms in genes associated with the unfolded protein response and neuronal structural maintenance. Moreover, genes involved in mitochondrial function and protein translation, which normally peak at sleep/wake transitions, peak instead at static times in schizophrenia, suggesting suboptimal timing of these essential processes that may contribute to cognitive deficits commonly found in schizophrenia.

neuroscience↗

bioRxiv2022

Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection

Circadian clocks are 24-hour endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub (https://github.com/circaPower/circaPower).

genomics↗

bioRxiv2020

The Suprachiasmatic Nucleus Regulates Anxiety-Like Behavior in Mice

Circadian rhythms are commonly disrupted in individuals with depression and/or anxiety disorders. Animal studies indicate that circadian rhythm disruption can cause increased depressive and anxiety-like behavior, but the underlying mechanisms are unclear. Currently, there is conflicting evidence as to whether the master pacemaker in the brain, the suprachiasmatic nucleus (SCN), plays a key role in regulating psychiatric-related behavior. To investigate the role of the SCN in regulating depressive and anxiety-like behavior in mice, we directly manipulated the neural activity of the SCN using two chronic optogenetic stimulation paradigms. Repeated stimulation of the SCN late in the active phase (circadian time 21, CT21) shortened the period and dampened the amplitude of homecage activity rhythms. Repeated stimulation of the SCN at unpredictable times during the dark phase dampened, fragmented and reduced the stability of homecage activity rhythms. In both SCN optogenetic stimulation paradigms, dampened homecage activity rhythms (decreased amplitude) was associated with increased measures of anxiety-like behavior, but not in control mice. Increased fragmentation and decreased day-to-day stability of homecage activity also correlated with increased anxiety-like behavior. Unexpectedly the change in period of homecage activity rhythms was not directly associated with any psychiatric-related behavior. Furthermore, we did not observe consistent correlations between homecage activity amplitude and depressive-like behavior in stimulated mice. Taken together, these results indicate that SCN-mediated dampening of rhythms is directly correlated with increased anxiety-like, but not depressive-like behavior in mice. This work is an important step in understanding how specific SCN neural activity disruptions affect mood and anxiety-related behavior.

neuroscience↗

bioRxiv2020

Genetic variation and sex differences are missed opportunities for addiction biology.

Concerns about external validity of rodent models and translation of findings across species are often based on narrow investigations of populations with limited diversity. Sources of individual variation - including genetics and sex - are only infrequently encompassed in model organism studies. As with most complex diseases, risk for cocaine use disorder is subject to considerable inter-individual variation. Explicit inclusion of individual differences in rodent research may reveal conserved phenotypes and molecular systems relevant to human addiction. We surveyed cocaine-related traits in both males and females of eight inbred mouse strains whose genomes collectively capture 90% of the genetic diversity of the mouse species. Across these strains, individual differences explained a substantial proportion of variance in cocaine-responsive or cocaine response-predictive behavioral and physiological phenotypes. Wild-derived mouse strains often extended the phenotypic ranges of these behaviors beyond what is observed in conventional laboratory strains. Striatum transcriptional responses to cocaine were also highly dependent upon strain and sex differences; most cocaine-responsive genes were differentially expressed in a manner moderated by strain, sex, or their combination. We compared the strain- and sex-mediated transcriptional responses to cocaine in mice to transcriptomic analysis of people with cocaine use disorder and found that mouse similarity to humans was highly dependent upon mouse genetic background and sex. Specifically, male WSB/EiJ mice and female NOD/ShiLtJ mice exhibited the greatest degree of neural transcriptional consilience with humans with cocaine use disorder. Model organism diversity thus represents a crucial source of biological information that can substantially improve external validity of neuropsychiatric research. Significance StatementLaboratory mice are widely used in research on neurobiological mechanisms of addiction, but most studies use a single strain and often sex of mice. To assess how individual differences in mice modulate addiction-related traits and how this impacts comparative analysis with humans, we studied cocaine-relevant behaviors and brain molecular correlates in both males and females of genetically diverse mouse strains. In this population, individual differences related to sex and/or genetics explain large proportions of differences in cocaine-related traits. Importantly, brain gene expression data demonstrated that some strains mimic human genomic states more readily than others. Individual differences thus represent a crucial and underdeveloped source of biological information about addiction mechanisms that may influence the translational utility of such studies.

neuroscience↗