Biology subjects

Berretta, S.

Publications and source records attributed to Berretta, S..

14 recordsLinked to original sources

bioRxiv2026

Aging-related Transcriptomic Changes with Spatial Resolution in the Human Prefrontal Cortex

The human prefrontal cortex (PFC), whose laminar organization is essential for cognitive function, is among the first regions to show age-related functional decline1,2. Single-cell sequencing studies revealed cell type-dependent aging effects but lacked spatial specificity3-6. Spatial transcriptomics (ST) advanced our molecular understanding of the human PFC7, yet whether aging-driven changes differ across PFC layers remains unclear. Here, we performed whole-transcriptome ST on postmortem PFC from 37 individuals across the adult lifespan. We mapped cortical layers and revealed aging mechanisms across layers. This represents one of the largest and most comprehensive lifespan ST analysis of the human PFC brain, offering crucial insight into how the brain ages and identifying potential molecular targets to mitigate cognitive aging and extend healthspan.

neuroscience↗

bioRxiv2025

A shared DNA-repeat toxicity threshold, reached somatically at cell-type-specific rates, unites cortical and striatal neurodegeneration in Huntingtons disease

Huntingtons disease (HD) affects two major brain areas - the striatum and cerebral cortex - in ways that differ in timing, severity, and gene-expression changes. For these reasons, and because many cortical neurons project axons to the affected striatal neurons, striatal and cortical atrophy have long been proposed to have distinct mechanisms, with one potentially a secondary consequence of the other. In the striatum, we recently found that neurons degenerate asynchronously as their own huntingtin (HTT) gene CAG-repeat tracts, typically inherited at 40-50 CAGs, expand somatically beyond 150 CAGs. To ask whether a similar or different dynamic affects the cerebral cortex, we analyzed HTT CAG repeats and genome-wide RNA expression together in more than 130,000 nuclei from 12 cortical areas of brain donors with HD. The resulting data revealed that cortical and striatal neurodegeneration in fact result from analogous sequences of cell-autonomous events, each instructed by somatic expansion of a neurons own HTT CAG repeat. Analyses revealed that somatic expansion beyond a high toxicity threshold (of about 150 CAGs) is necessary and sufficient to initiate pathological changes; that this pathogenicity length threshold is shared by striatal and cortical projection neurons of all types; and that cortical area, cortical layer, and axonal projections play only incidental roles, as proxies for the true driver: profound (up to 50-fold) variation among types and subtypes of pyramidal neurons in the likelihood of reaching the 150-CAG toxicity threshold in a human lifetime. These results also suggest that containing somatic DNA-repeat expansion below this high toxicity threshold would protect both brain areas in HD.

genetics↗

bioRxiv2025

Genetics-to-structure multiscale analysis identifies disrupted calcium homeostasis as a mechanism of psychiatric disease

Neuropsychiatric disorders are highly heritable, but the molecular mechanisms linking risk variants to disease remain unclear1. Linking genetics to biological mechanisms requires integrating evidence across scales, from sequence variation to gene regulation to protein function. Here we integrate genetic, transcriptomic, and structural evidence to identify dysregulation of neuronal Ca2+ dynamics as a contributing mechanism. We analyzed single-nucleus neuronal RNA-seq data together with genome-wide association study (GWAS) heritability in a new way to identify gene expression programs enriched for psychiatric risk; genes encoding Ca2+ flux pathway genes were implicated by this analysis, a result that was then confirmed by concentrations of rare coding variants in these same genes in persons with psychiatric disorders. A critical gene in this biology, ATP2B2, encodes a Ca2+-extruding ATPase pump2 linked to neuropsychiatric disorders primarily through missense variants. To recognize specific molecular functions affected by these missense variants, we developed a 3D-neighborhood-based method that maps missense variants onto AlphaFold3-predicted protein structures and tests clustering of protein-altering variants in three-dimensional space. This approach revealed clustering of these missense changes in the Ca2+ pore and ATP:Mg2+ coordination site of ATP2B2. To validate the structural predictions arising from the genetic analysis, we determined the structure of human Ca2+-bound ATP2B2 at 2.64 [A] resolution by cryogenic electron microscopy. The structure replicated the 3D mutational hotspots identified by the genetic analysis, supporting the observation that neuropsychiatric variants cluster near specific catalytic sites of ATP2B2. In vitro experiments revealed that missense variants prioritized by the structural clustering analysis impaired ATP2B2-mediated Ca2+ extrusion in cellular and biochemical assays. Together, these findings suggest that precise regulation of Ca2+ dynamics is a contributing mechanism in neuropsychiatric disorders and establish a structure-based framework for predicting the mechanistic impact of missense variants.

genetics↗

bioRxiv2025

Nociceptin receptor and ligand in Alzheimer's disease:Implications for psychiatric symptoms and circadianregulation

BackgroundNociceptin (N/OFQ) and its receptor OPRL1 play crucial roles in emotional processing, reward-related behaviors, learning, and neurotransmitter regulation, but their involvement in Alzheimers disease (AD) pathology remains poorly understood. This study investigated possible relationships between prepronociceptin (PNOC) and OPRL1 expression and psychiatric symptoms in AD, utilizing Natural Language Processing (NLP) to assess Research Domain Criteria (RDoC) domains. MethodsPost-mortem brain tissue from the dorsal anterior cingulate gyrus (BA32) was analyzed in 61 donors across different Braak and Braak (B&B) stages. RNA expression of PNOC and OPRL1 was quantified and correlated with RDoC scores derived from medical records using NLP. Sex-stratified analyses, circadian rhythmicity analysis, and cell-type specific expression patterns were examined. ResultsBoth genes showed significant downregulation in AD cases (PNOC: p = 0.024; OPRL1: p < 0.001), with notable sex differences. Men displayed higher post-mortem PNOC (Cohens d = -0.482) and OPRL1 (Cohens d = -0.237) expression compared to women. In adjusted models controlling for B&B stage and post-mortem interval, PNOC expression significantly correlated with dimensional scores of positive valence ({beta} = -0.38, p = 0.035) and arousal regulatory systems ({beta} = -0.43, p = 0.015) derived from a text classification algorithm applied to medical records. OPRL1 showed disrupted circadian rhythmicity in AD cases (p = 0.151 vs. p = 0.020 in controls). ConclusionsThese findings suggest distinct roles for PNOC and OPRL1 in AD pathology, with PNOC primarily associated with psychiatric symptoms and OPRL1 showing disrupted circadian regulation. Sex-specific expression patterns further indicate the need for personalized therapeutic approaches targeting the nociceptin system.

neuroscience↗

bioRxiv2025

Nociceptin Orphanin F/Q Pathways are Dysregulated by Stress and Modulate Reward Learning and Motivation Across Species

Nociceptin orphanin F/Q has been implicated in stress-related depressive phenotypes. Specifically, exposure to chronic stressors upregulates nociceptin receptors (NOPR), whereas NOPR antagonism has anti-depressant/anti-anhedonic effects. The mechanisms underlying these effects remain, however, unclear. Here, we investigated the role of NOPR in depressive phenotypes alongside potentially prohedonic effects of NOPR antagonism across species. In Study 1, we evaluated whether exposure to early-life adversity (ELA) upregulated ventral tegmental area (VTA) and striatal prepronociceptin (Pnoc) gene expression in adult mice. In Study 2, we tested whether chronic social defeat altered Pnoc gene expression in reward-related regions. To establish whether direct NOPR modulation is implicated in reward-related behaviors, in Study 3, we assessed whether NOPR antagonism alters reward learning in rats. Finally, in Study 4, we tested whether NOPR antagonism boosts motivation among depressed humans. ELA induced anhedonic behavior and increased Pnoc expression in the VTA; in females (but not males), ELA increased Pnoc expression in the dorsal striatum (Study 1). Furthermore, chronic stress reduced Pnoc-expressing cells in the VTA, dorsal striatum and prefrontal cortex and susceptible rats showed reduced VTA NOPR gene (Oprl1)-expressing cells (Study 2). In a behavioral assay, a single 30-mg dose of a NOPR antagonist (BTRX-246040) boosted reward learning in rats (Study 3). Finally, in depressed humans, relative to placebo, 8-week treatment with BTRX-246040 increased incentive motivation (Study 4). Collectively, our findings indicate that chronic stressors alter Pnoc and mRNA levels of Pnoc-expressing cells in a sex-selective and region-specific manner impacting reward structures, and that NOPR antagonism shows anti-anhedonic properties.

neuroscience↗

bioRxiv2024

Long somatic DNA-repeat expansion drives neurodegeneration in Huntington disease

Huntington Disease (HD) is a fatal genetic disease in which most striatal projection neurons (SPNs) degenerate. The central biological question about HD pathogenesis has been how the disease-causing DNA repeat expansion (CAGn) in the huntingtin (HTT) gene leads to neurodegeneration after decades of apparent latency. Inherited HTT alleles with a longer CAG repeat hasten disease onset; the length of this repeat also changes over time, generating somatic mosaicism, and genes that regulate DNA-repeat stability can influence HD age-at-onset. To understand the relationship between a cells CAG-repeat length and its biological state, we developed a single-cell method for measuring CAG-repeat length together with genome-wide RNA expression. We found that the HTT CAG repeat expands from 40-45 CAGs to 100-500+ CAGs in HD-vulnerable SPNs but not in other striatal cell types, with these long DNA-repeat expansions acquired at different times by individual SPNs. Surprisingly, somatic expansion from 40 to 150 CAGs had no apparent effect upon gene expression - but neurons with 150-500+ CAGs shared profound gene-expression changes. These expression changes involved hundreds of genes, escalated alongside further CAG-repeat expansion, eroded positive and then negative features of neuronal identity, and culminated in expression of senescence/apoptosis genes. Rates of striatal neuron loss across HD stages reflected the rates at which neurons entered this biologically distorted state. Our results suggest that HTT CAG repeats in striatal neurons undergo decades of biologically quiet expansion, then, as they asynchronously cross a high threshold, cause SPNs to degenerate quickly and asynchronously. We conclude that, at any moment in the course of HD, most neurons have an innocuous (but unstable) huntingtin gene, and that HD pathogenesis is a DNA process for almost all of a neurons life.

genetics↗

bioRxiv2024

Interneuron loss and microglia activation by transcriptome analyses in the basal ganglia of Tourette syndrome

Tourette syndrome (TS) is a disorder of high-order integration of sensory, motor, and cognitive functions afflicting as many as 1 in 150 children and characterized by motor hyperactivity and tics. Despite high familial recurrence rates, a few risk genes and no biomarkers have emerged as causative or predisposing factors. The syndrome is believed to originate in basal ganglia, where patterns of motor programs are encoded. Postmortem immunocytochemical analyses of brains with severe TS revealed decreases in cholinergic, fast-spiking parvalbumin, and somatostatin interneurons within the striatum (caudate and putamen nuclei). Here, we performed single cell transcriptomic and chromatin accessibility analyses of the caudate nucleus from 6 adult TS and 6 control post-mortem brains. The data reproduced the known cellular composition of the adult human striatum, including a majority of medium spiny neurons (MSN) and small populations of GABAergic and cholinergic interneurons. Comparative analysis revealed that interneurons were decreased by roughly 50% in TS brains, while no difference was observed for other cell types. Differential gene expression analysis suggested that mitochondrial function, and specifically oxidative metabolism, in MSN and synaptic function in interneurons are both impaired in TS subjects. Furthermore, such an impairment was coupled with activation of immune response pathways in microglia. Also, our data explicitly link gene expression changes to changes in cis-regulatory activity in the corresponding cell types, suggesting de-regulation as a factor for the etiology of TS. These findings expand on previous research and suggest that impaired modulation of striatal function by interneurons may be the origin of TS symptoms.

neuroscience↗

bioRxiv2024

Concerted neuron-astrocyte gene expression declines in aging and schizophrenia

Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a striking relationship between peoples cortical neurons and cortical astrocytes. We used single-nucleus RNA-seq to analyze the prefrontal cortex of 191 human donors ages 22-97 years, including healthy individuals and persons with schizophrenia. Latent-factor analysis of these data revealed that in persons whose cortical neurons more strongly expressed genes for synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the Synaptic Neuron- and-Astrocyte Program (SNAP). In schizophrenia and aging - two conditions that involve declines in cognitive flexibility and plasticity 1,2 - cells had divested from SNAP: astrocytes, glutamatergic (excitatory) neurons, and GABAergic (inhibitory) neurons all reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy persons of similar age, may underlie many aspects of normal human interindividual differences and be an important point of convergence for multiple kinds of pathophysiology.

neuroscience↗

bioRxiv2023

Dimensional clinical phenotyping using post-mortem brain donor medical records: Association with neuropathology

INTRODUCTIONTransdiagnostic dimensional phenotypes are essential to investigate the relationship between continuous symptom dimensions and pathological changes. This is a fundamental challenge to postmortem work, as assessment of newly developed phenotypic concepts needs to rely on existing records. METHODSWe adapted well-validated methodologies to compute NIMH research domain criteria (RDoC) scores using natural language processing (NLP) from electronic health records (EHRs) obtained from post-mortem brain donors and tested whether RDoC cognitive domain scores were associated with hallmark Alzheimers disease (AD) neuropathological measures. RESULTSOur results confirm an association of EHR-derived cognitive scores with hallmark neuropathological findings. Notably, higher neuropathological load, particularly neuritic plaques, was associated with higher cognitive burden scores in the frontal ({beta}=0.38, p=0.0004), parietal ({beta}=0.35, p=0.0008), temporal ({beta}=0.37, p=0. 0004) and occipital ({beta}=0.37, p=0.0003) lobes. DISCUSSIONThis proof of concept study supports the validity of NLP-based methodologies to obtain quantitative measures of RDoC clinical domains from postmortem EHR.

neuroscience↗

bioRxiv2023

SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration

High levels of proinflammatory cytokines induce neurotoxicity and catalyze inflammation-driven neurodegeneration, but the specific release mechanisms from microglia remain elusive. We demonstrate that secretory autophagy (SA), a non-lytic modality of autophagy for secretion of vesicular cargo, regulates neuroinflammation-mediated neurodegeneration via SKA2 and FKBP5 signaling. SKA2 inhibits SA-dependent IL-1{beta} release by counteracting FKBP5 function. Hippocampal Ska2 knockdown in mice hyperactivates SA resulting in neuroinflammation, subsequent neurodegeneration and complete hippocampal atrophy within six weeks. The hyperactivation of SA increases IL-1{beta} release, initiating an inflammatory feed-forward vicious cycle including NLRP3-inflammasome activation and Gasdermin D (GSDMD)-mediated neurotoxicity, which ultimately drives neurodegeneration. Results from protein expression and co-immunoprecipitation analyses of postmortem brains demonstrate that SA is hyperactivated in Alzheimers disease. Overall, our findings suggest that SKA2-regulated, hyperactive SA facilitates neuroinflammation and is linked to Alzheimers disease, providing new mechanistic insight into the biology of neuroinflammation.

neuroscience↗

bioRxiv2022

A marmoset brain cell census reveals persistent influence of developmental origin on neurons

The mammalian brain is composed of many brain structures, each with its own ontogenetic and developmental history. Transcriptionally-based cell type taxonomies reveal cell type composition and similarity relationships within and across brain structures. We sampled over 2.4 million brain cells across 18 locations in the common marmoset, a New World monkey primed for genetic engineering, and used single-nucleus RNA sequencing to examine global gene expression patterns of cell types within and across brain structures. Our results indicate that there is generally a high degree of transcriptional similarity between GABAergic and glutamatergic neurons found in the same brain structure, and there are generally few shared molecular features between neurons that utilize the same neurotransmitter but reside in different brain structures. We also show that in many cases the transcriptional identities of cells are intrinsically retained from their birthplaces, even when they migrate beyond their cephalic compartments. Thus, the adult transcriptomic identity of most neuronal types appears to be shaped much more by their developmental identity than by their primary neurotransmitter signaling repertoire. Using quantitative mapping of single molecule FISH (smFISH) for markers for GABAergic interneurons, we found that the similar types (e.g. PVALB+ interneurons) have distinct biodistributions in the striatum and neocortex. Interneuron types follow medio-lateral gradients in striatum but form complex distributions across the neocortex that are not described by simple gradients. Lateral prefrontal areas in marmoset are distinguished by high relative proportions of VIP+ neurons. We further used cell-type-specific enhancer driven AAV-GFP to visualize the morphology of molecularly-resolved interneuron classes in neocortex and striatum, including the previously discovered novel primate-specific TAC3+ striatal interneurons. Our comprehensive analyses highlight how lineage and functional class contribute to the transcriptional identity and biodistribution of primate brain cell types. One-Sentence SummaryAdult primate neurons are imprinted by their region of origin, more so than by their functional identity.

neuroscience↗

bioRxiv2021

Proteoglycan Clusters as a Site of Coordinated, Multi-Dendritic Plasticity

Experience-dependent learning depends on synaptic plasticity. While plasticity in individual synapses has been extensively investigated, the mechanisms underlying coordinated changes across sets of synapses on multiple dendrites, likely needed to encode effective adaptations to a salient stimulus, are not well understood. The extracellular matrix is uniquely well suited to fulfill this function, as rapid glia-driven remodeling of its local composition powerfully impact synaptic plasticity. We show that extracellular matrix microenvironments, named CS6 clusters, dynamically form around several dendrites in response to sensory stimuli in coincidence to stimulus-driven synaptic plasticity. CS6 clusters, formed by glia-dependent secretion of extracellular matrix components surrounding sets of adjacent dendrites, may represent a novel structure supporting coordinated synaptic plasticity. One Sentence SummaryExtracellular matrix clusters form microenvironments for coordinated multi-dendrite synaptic plasticity.

neuroscience↗

bioRxiv2020

Microglial Associated Circadian Rhythms of Perineuronal Net Composition

Perineuronal Nets (PNNs) are extracellular matrix (ECM) structures that envelop neurons and regulate synaptic functions. Long thought to be stable structures, PNNs have been recently shown to respond dynamically during learning, potentially regulating the formation of new synapses. We postulated that PNNs vary during sleep, a period of active synaptic modification. Notably, PNN components are cleaved by matrix proteases such as the protease cathepsin-S. This protease is diurnally expressed in the mouse cortex, coinciding with dendritic spine density rhythms. Thus, cathepsin-S may contribute to PNN remodeling during sleep, mediating synaptic reorganization. These studies were designed to test the hypothesis that PNN numbers vary in a diurnal manner in the rodent and human brain, as well as in a circadian manner in the rodent brain, and that these rhythms are disrupted by sleep deprivation. In mice, we observed diurnal and circadian rhythms of PNNs labeled with the lectin wisteria floribunda agglutinin (WFA+PNNs) in several brain regions involved in emotional memory processing. Sleep deprivation prevented the daytime decrease of WFA+ PNNs and enhances fear memory extinction. Diurnal rhythms of cathepsin-S expression in microglia were observed in the same brain regions, opposite to PNN rhythms. Finally, incubation of mouse sections with cathepsin-S eliminated PNN labeling. In humans, WFA+PNNs showed a diurnal rhythm in the amygdala and thalamic reticular nucleus (TRN). Our results demonstrate that PNNs vary in a circadian manner and this is disrupted by sleep deprivation. We suggest that rhythmic modification of PNNs may contribute to memory consolidation during sleep.

neuroscience↗

bioRxiv2019

Innovations in Primate Interneuron Repertoire

Primates and rodents, which descended from a common ancestor more than 90 million years ago, exhibit profound differences in behavior and cognitive capacity. Modifications, specializations, and innovations to brain cell types may have occurred along each lineage. We used Drop-seq to profile RNA expression in more than 184,000 individual telencephalic interneurons from humans, macaques, marmosets, and mice. Conserved interneuron types varied significantly in abundance and RNA expression between mice and primates, but varied much more modestly among primates. In adult primates, the expression patterns of dozens of genes exhibited spatial expression gradients among neocortical interneurons, suggesting that adult neocortical interneurons are imprinted by their local cortical context. In addition, we found that an interneuron type previously associated with the mouse hippocampus--the \"ivy cell\", which has neurogliaform characteristics--has become abundant across the neocortex of humans, macaques, and marmosets. The most striking innovation was subcortical: we identified an abundant striatal interneuron type in primates that had no molecularly homologous cell population in mouse striatum, cortex, thalamus, or hippocampus. These interneurons, which expressed a unique combination of transcription factors, receptors, and neuropeptides, including the neuropeptide TAC3, constituted almost 30% of striatal interneurons in marmosets and humans. Understanding how gene and cell-type attributes changed or persisted over the evolutionary divergence of primates and rodents will guide the choice of models for human brain disorders and mutations and help to identify the cellular substrates of expanded cognition in humans and other primates.

neuroscience↗