Biology subjects

Zhou, Z.

Publications and source records attributed to Zhou, Z..

At least 181 records · Page 10Linked to original sources

bioRxiv2024

CircAge: A Comprehensive Resource for Aging-Associated Circular RNAs Across Species and Tissues

Circular RNAs (circRNAs) represent a novel class of RNA molecules characterized by a circular structure and enhanced stability. Emerging evidence indicates that circRNAs play pivotal regulatory roles in the aging process. Despite this, there is a lack of a systematic resource that integrates aging-associated circRNA data. Therefore, we developed a comprehensive database named circAge, which encompasses 689 aging-related samples from 7 species and 21 tissue types. We also generated 47 new tissue samples from mice and rhesus monkeys through high-throughput sequencing. Integrating predictions from multiple bioinformatics tools, we identified over 413,378 unique circRNAs. Our data analysis revealed a general increase in circRNA expression levels with age, with approximately 22% of circRNAs demonstrating sequence conservation across species. The circAge database systematically predicts potential interactions between circRNAs and miRNAs, RNA-binding proteins, and assesses the coding potential of circRNAs. This resource lays a foundation for elucidating the regulatory mechanisms of circRNAs in aging. As a comprehensive repository of aging-associated circRNAs, circAge will significantly accelerate research in this field, facilitating the discovery of novel biomarkers and therapeutic targets for aging biology and developing diagnostic and therapeutic strategies for aging and age-related diseases. CircAge is publicly available at https://circage.kiz.ac.cn.

bioinformatics↗

bioRxiv2024

Impact of oral Chlamydia Vaccination on Host Gut Microbiome and Metabolites Composition

Chlamydia trachomatis, an intracellular pathogen, is recognized as the most common sexually transmitted bacterial infection among women worldwide. Chlamydia infections can lead to undesirable clinical outcomes, including pelvic inflammatory disease and infertility. Recently, the gut has been identified as a niche for Chlamydia colonization; however, despite the biological impact on the host remaining under investigation, oral inoculation of Chlamydia as a whole-organism vaccine has been reported as a promising strategy for preventing genital Chlamydia infections. Few studies have evaluated the impact of oral Chlamydia vaccination on the gut microbiome and metabolite changes. In this study, we assessed time-series alterations in the gut microbiome and metabolites following oral Chlamydia inoculation, and we analyzed the composition and correlation between serum immune parameters and the sequencing profiles in the host. We identified 129 microbial changes and 186 significantly different metabolites in the gut across various vaccination approaches during the 30-day immunization process. Additionally, we discussed potential biomarkers of effective immunization based on correlation analysis. IMPORTANCEChlamydia infections primarily lead to morbidity rather than mortality. Consequently, in developing and implementing a Chlamydia vaccine, the utmost priority is ensuring safety. As a promising yet controversial approach, live oral vaccination for Chlamydia raises concerns regarding its impact on the hosts gut environment. Our study not only investigates changes in the gut microbiome and metabolites during vaccination but also identifies potential biomarkers during immunization. These findings are crucial for the development of whole-organism oral Chlamydia vaccines and provide valuable insights into the long-term colonization of Chlamydia in the gut.

microbiology↗

bioRxiv2024

Geographic-specific Diversification of Vaginal Microbiota in China

The vaginal microbiota is pivotal to womens reproductive health, with significant geographic and ethnic heterogeneity suggesting evolutionary adaptations to environmental, climatic, and lifestyle factors. In this multi-centric study, we analyzed vaginal microbiome samples from women across five provinces in China, each characterized by distinct climatic, ethnic, and lifestyle traits. Our results indicate that the vaginal microbiota among Chinese women is characterized by low alpha diversity, with Lactobacillus crispatus being the dominant species in Community State Type (CST) I, especially in the northern regions. While most participants exhibited stable CSTs throughout their menstrual cycles, fluctuations were observed in some individuals. We also detected low-abundance bacterial species such as Fannyhesea vaginae and Sneathia vaginalis. Comparative genomic analysis of high-quality metagenome-assembled genomes of L. crispatus revealed minimal single nucleotide polymorphism (SNP) variations within individuals but substantial diversity between individuals, delineating a distinct separation between vaginal-associated populations (VAP) and gut-associated populations (GAP). These findings highlight the intricate dynamics of the vaginal microbiome, which are markedly influenced by geographic and individual determinants. This study offers an in-depth phylogenetic and genomic analysis of the vaginal microbiota among Chinese women, underscoring the imperative for further research into the impact of regional and individual variations on microbial community composition. Such knowledge could facilitate the development of personalized vaginal health management strategies that accommodate the unique microbiome profiles specific to different geographical regions. ImportanceThis study provides a groundbreaking analysis of the vaginal microbiota among Chinese women, offering insights into the population structure and evolutionary dynamics of this critical component of womens reproductive health. The research reveals that Lactobacillus crispatus, a key species in vaginal health, has a recent evolutionary emergence and exhibits significant geographic variation in prevalence, being more common in northern China. This discovery, along with the identification of distinct vaginal-associated and gut-associated populations, underscores the importance of understanding the vaginal microbiotas complexity. The findings have profound implications for developing personalized strategies to manage vaginal health, tailored to regional microbiome characteristics. This work not only advances our understanding of the vaginal microbiotas role in health and disease but also sets the stage for future research into the factors that shape microbial community structures across diverse populations.

microbiology↗

bioRxiv2024

PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation

Hearing loss is one of the most prevalent sensory disorders, but no commercial biological treatments are currently available. Here, we identified an East Asia-specific founder mutation, the homozygous c.220C>T mutation in MPZL2, that contributes to a significant proportion of hereditary deafness cases in our cohort study. We found that the disease-causing mutation could be targetable by adenine base editors (ABEs) that enable A{middle dot}T-to-G{middle dot}C base corrections without DNA double-strand breaks. To demonstrate this, we developed a humanized mouse model (hMPZL2Q74X/Q74X) that recapitulates human MPZL2 deafness and leads to progressive hearing loss. A PAM-flexible ABE variant with reduced bystander and off-target effects (ABE8eWQ-SpRY:sgRNA3) was packaged in dual adeno-associated viruses (AAVs) and injected into the inner ear of hMPZL2Q74X/Q74X mice and effectively corrected the mutation. This treatment significantly restored hearing function, improved inner ear structural integrity, and reversed altered gene expression. Base editing may hold therapeutic potential for hereditary deafness, including most cases of MPZL2 deafness.

genetics↗

bioRxiv2024

Iridescent structural coloration in a crested Cretaceous enantiornithine bird from Jehol Biota

A combination of sectioning and microscopy techniques, along with the application of finite-difference-time-domain modeling on a fossil feather, results in the novel estimation of the range of iridescent colors from the fossilized melanosome type and organization preserved in the elongate head crest feathers of a new Cretaceous enantiornithine bird. The densely packed rod-like melanosomes are estimated to have yielded from red to deep blue iridescent coloration of the head feathers. The shape and density of these melanosomes also may have further increased the feathers structural strength. This occurrence on a likely male individual is highly suggestive of both a signaling function of the iridescent crest, and a potential behavioral role in adjusting the angle of light incidence to control the display of this iridescent structural coloration.

evolutionary biology↗

bioRxiv2024

Expression study of Krabbe Disease GALC missense variants -- Insights from quantification profiles of residual enzyme activity, secretion and psychosine levels

Krabbe disease (KD) is an autosomal recessive lysosomal storage disorder caused by loss-of-function mutations in the GALC gene, which encodes for the enzyme galactosylceramidase (GALC). GALC is crucial for myelin metabolism. Functional deficiency of GALC leads to toxic accumulation of psychosine, dysfunction and death of oligodendrocytes, and eventual brain demyelination. To date, 46 clinically-relevant, pathogenic GALC missense mutations (MMs) have been identified in KD patients. These MMs are present in [~]70% of KD cases reported over 8 published studies between 1996 - 2019. However, the mechanisms by which these MMs lead to GALC functional deficiency and their correlations with clinical phenotype remain poorly understood. To address this, we generated a GALC-knockout human oligodendrocytic cell line (MO3.13/ GALC-KO) using CRISPR-Cas9 method to assess GALC function and GALC secretion. We evaluated 5 polymorphic and 31 clinically-relevant MM variants (MMVs) using transient expression assays. Our results showed that 26 MMVs, including 10 co-variants with p.I562T, reduced GALC activity by 92% - 100% compared to wild-type GALC (WT-GALC). MMVs from infantile-onset KD patients produced < 2% of WT activity, whereas those associated with juvenile- and adult-onset cases retained up to 7% of WT activity. Residual GALC activity was correlated with mature, lysosomal GALC protein levels (Pearson r = 0.93, P<0.0001). Many low-activity MMVs did not correspondingly impair GALC secretion. Twenty-one of the 26 low-activity MMVs showed a 21% - 100% reduction in sec-GALC levels, indicating varying degrees of GALC mis-trafficking among these variants. Importantly, GALC activity among MMVs strongly correlates with clinical disease severity, based on the age of symptom onset in patients with either homozygous MM (Pearson r = 0.98, P<0.0001, n = 7) or compound heterozygous (Pearson r = 0.94, P<0.0001, n = 12) MM-null mutation genotypes. Thus, our data suggests that GALC activity could serve as a prognostic disease indicator under specific experimental conditions. We further investigated the impact of pathogenic MMVs on psychosine accumulation, a key biomarker for KD. Psychosine levels were 21-fold higher in mock control cells compared to WT-GALC transfected cells (mock = 0.349 pmol/mg, WT-GALC = 0.016 pmol/mg), but negatively correlated with GALC activity among pathogenic MMVs (Pearson r = -0.63, P < 0.01, n = 15). Although psychosine levels were higher in most MMVs associated with infantile-onset KD, no significant correlations with clinical onset were detected. Overall, our study provides a comprehensive quantitative analysis of the functional deficits and mis-trafficking associated with clinically-relevant GALC MMVs, enhancing our understanding of the molecular genetics and genotype-phenotype correlations of the GALC gene in Krabbe disease.

cell biology↗

bioRxiv2024

Scaling laws of plasmids across the microbial tree of life

Plasmids play a critical role in shaping the dynamics and evolution of microbial communities. The capacity of a plasmid to express genes is constrained by two parameters: length and copy number. However, the interplay between these parameters and their constraints on plasmid evolution have remained elusive due to the absence of comprehensive quantitative analyses. To address this gap, we developed Probabilistic Iterative Read Assignment (PIRA), a new computational method that overcomes previous computational bottlenecks, enabling rapid and accurate determination of plasmid copy numbers at an unprecedented scale. Applying PIRA to all microbial genomes in the NCBI RefSeq database with linked short-read sequencing data in the Sequencing Read Archive (SRA), we analyzed 4,317 bacterial and archaeal genomes encompassing 11,338 plasmids, spanning the microbial tree of life. Our analysis reveals three scaling laws of plasmids: first, an inverse power-law correlation between plasmid copy number and plasmid length; second, a positive linear correlation between protein-coding genes and plasmid length; and third, a positive correlation between metabolic genes per plasmid and plasmid length, particularly for large plasmids. These scaling laws imply fundamental constraints on plasmid evolution and functional organization, indicating that as plasmids increase in length, they converge toward chromosomal characteristics in copy number and functional content. Our findings not only advance the understanding of plasmid dynamics but also have implications for microbial evolution, biotechnology, and the design of synthetic plasmids. SignificanceBy discovering universal scaling laws and developing a new computational method to compute plasmid copy numbers across the microbial tree of life, we show that as plasmids increase in length, they converge to chromosomes in their copy number and their coding and metabolic properties. This insight reveals fundamental principles governing plasmid evolution and has implications for biotechnology and medicine.

microbiology↗

bioRxiv2024

Neuronal loss of Galnt2 Impairs O-glycosylation and Leads to Neurobehavioral Deficits Mimicking GALNT2-CDG

GALNT2-CDG is a multi-system genetic disorder due to biallelic pathogenic mutations in GALNT2, which encodes a ubiquitously expressed Golgi-localized glycosyltransferase that initiates mucin-type O-glycosylation. Affected individuals exhibit dysmorphic facial features, short stature, decreased HDL-C, and notable impairments in brain function. GALNT2-CDG patients show global developmental delay without speech development, childhood epilepsy, autistic-like features, and white-matter brain abnormalities. The extent of O-glycosylation in brain development and function remains poorly understood. To address this question, we selectively ablated Galnt2 from pan-neuronal cells in the brain and found that conditional knockout mice exhibit deficits across numerous behavioral domains, including locomotion, motor coordination, sociability, learning, and memory, as well as experience spontaneous seizures, recapitulating characteristic neurological manifestations of GALNT2-CDG. Given the catalytic activity of GALNT2 to initiate mucin-type O-glycosylation, we used glycoproteomics to identify disrupted O-glycosylation in synaptosomes purified from cortical tissues. We ascertained a non-redundant, isoform-specific contribution of GALNT2 to the cortical synaptosomal O-glycoproteome, identifying candidate glycoproteins and disrupted O-glycosites that accompany behavioral abnormalities in knockout mice. These findings demonstrate functional impact of O-glycosylation in neurons, implicating roles of O-glycosylation in diverse molecular and cellular pathways related to neuronal function and provide new opportunities to gain insights into the neurological pathophysiology of GALNT2-CDG.

neuroscience↗

bioRxiv2024

Cell-type-informed genotyping of mosaic focal epilepsies reveals cell-autonomous and non-cell-autonomous disease-associated transcriptional programs

Recent studies demonstrate growing roles for genetic mosaicism in neurodevelopmental and neuropsychiatric disorders, with the paradigm being drug-resistant pediatric focal epilepsy related to activating somatic variants in the PI3K-mTOR pathway. While identifying the genotype-associated changes at the single-cell level is fundamental to understanding disease pathophysiology, this remains technically challenging in human tissue samples with existing methods. Here, we performed single-nucleus RNA-sequencing (snRNA-seq) of 20 focal cortical dysplasia (FCD) samples removed surgically for treatment of drug-resistant epilepsy, and 10 non-FCD controls, and we developed a new approach, Genotyping Of Transcriptomes Enhanced with Nanopore sequencing (GO-TEN), that combines targeted complementary (c)DNA sequencing with snRNA-seq to perform concurrent single-nucleus genotyping and transcriptional analysis. We find that mosaic pathogenic variants in FCD do not produce a detectable novel cell identity, but instead we observe conserved cell types present both in FCD cases and non-FCD control specimens. Similarly, GO-TEN analysis shows that most pathogenic variant-carrying cells have well-differentiated neuronal or glial identities and are enriched for layer II-III excitatory neurons. We identify cell-intrinsic disruption of glutamate and GABA-A signaling pathways in variant-carrying neurons and altered intercellular signaling, making potential mechanisms for epileptogenesis in FCD. In summary, by addressing genotype-specific changes in mosaic epilepsy-associated lesions, our study highlights new potential disease mechanisms and therapeutic targets.

genetics↗

bioRxiv2024

Multi-View Integrative Approach For Imputing Short-Chain Fatty Acids and Identifying Key factors predicting Blood SCFA

Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fiber within gastrointestinal tract. SCFAs produced by gut microbiotas (GMs) are absorbed by host, reach bloodstream, and are distributed to different organs, thus influencing host physiology. However, due to the limited budget or the poor sensitivity of instruments, most studies on GMs have incomplete blood SCFA data, limiting our understanding of the metabolic processes within the host. To address this gap, we developed an innovative multi-task multi-view integrative approach (M2AE, Multi-task Multi-View Attentive Encoders), to impute blood SCFA levels using gut metagenomic sequencing (MGS) data, while taking into account the intricate interplay among the gut microbiome, dietary features, and host characteristics, as well as the nuanced nature of SCFA dynamics within the body. Here, each view represents a distinct type of data input (i.e., gut microbiome compositions, dietary features, or host characteristics). Our method jointly explores both view-specific representations and cross-view correlations for effective predictions of SCFAs. We applied M2AE to two in-house datasets, which both include MGS and blood SCFAs profiles, host characteristics, and dietary features from 964 subjects and 171 subjects, respectively. Results from both of two datasets demonstrated that M2AE outperforms traditional regression-based and neural-network based approaches in imputing blood SCFAs. Furthermore, a series of gut bacterial species (e.g., Bacteroides thetaiotaomicron and Clostridium asparagiforme), host characteristics (e.g., race, gender), as well as dietary features (e.g., intake of fruits, pickles) were shown to contribute greatly to imputation of blood SCFAs. These findings demonstrated that GMs, dietary features and host characteristics might contribute to the complex biological processes involved in blood SCFA productions. These might pave the way for a deeper and more nuanced comprehension of how these factors impact human health.

bioinformatics↗

bioRxiv2024

Excitatory and Inhibitory Effects of Saphenous Nerve Stimulation on Two Different Bladder Conditons: Underactivity and Overactivity

BackgroundThis study aimed at exploring the effects of saphenous nerve stimulation (SNS) on treating both overactive bladder (OAB) and underactive bladder (UAB). MethodIn 6 -chloralose anesthetized cats, bipolar nerve cuff electrodes were implanted on the saphenous nerve and pudendal nerve. UAB was induced by pudendal nerve stimulation (PNS) at 5Hz, 2 threshold (T) and OAB was induced by infusion of 0.25% acetic acid (AA). Multiple cystometrograms (CMGs) were performed to investigate the effects of SNS on pathological bladder at 1Hz and 20Hz, respectively. ResultsApplication of PNS (5Hz, 2T) induced UAB by significantly increasing the bladder capacity (BC) to 156.3%{+/-}9.8% of control level, while combination of PNS and SNS (1Hz, 2T) applied during CMGs normalized the bladder underactivity by significantly reducing the BC to 93.6%{+/-}9.5% (P =0.026). Moreover, the BC was reduced to 64.1%{+/-}5.4% of control after infusion of AA, and SNS at 20Hz, 6T significantly increased the BC back to 93.4%{+/-}6.3% (P =0.005). No post-stimulation effect of SNS was detected at both 1Hz and 20Hz. However, there were no significant changes of contraction amplitude and duration during stimulation. ConclusionIn this study, we confirmed the frequency-dependence of SNS in regulating pathological bladder in cats. It provided experimental evidence for treating both OAB and UAB using SNS in clinic.

physiology↗

bioRxiv2024

Harmonization of Structural Brain Connectivity through Distribution Matching

The increasing prevalence of multi-site diffusion-weighted magnetic resonance imaging (dMRI) studies potentially offers enhanced statistical power to investigate brain structure. However, these studies face challenges due to variations in scanner hardware and acquisition protocols. While several methods for dMRI data harmonization exist, few specifically address structural brain connectivity. We introduce a new distribution-matching approach to harmonizing structural brain connectivity across different sites and scanners. We evaluate our method using structural brain connectivity data from three distinct datasets (OASIS-3, ADNI-2, and PREVENT-AD), comparing its performance to the widely used ComBat method and the more recent CovBat approach. We examine the impact of harmonization on the correlation of brain connectivity with the Mini-Mental State Examination score and age. Our results demonstrate that our distribution-matching technique effectively harmonizes structural brain connectivity while maintaining non-negativity of the connectivity values, and produces correlation strengths and significance levels competitive with alternative approaches. Qualitative assessments illustrate the desired distributional alignment across datasets, while quantitative evaluations confirm competitive performance. This work contributes to the growing field of dMRI harmonization, potentially improving the reliability and comparability of structural connectivity studies that combine data from different sources in neuroscientific and clinical research.

bioengineering↗

bioRxiv2024

ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers

ATP-dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. Here, we investigate effects of two major remodelers, ACF and RSC using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on pre-formed chromatin condensates. ACF spaces nucleosomes without de-condensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. In contrast, RSC catalyzes ATP-dependent de-condensation of chromatin. Surprisingly, RSC also drives micron-scale movements of entire condensates. These newly uncovered activities of RSC explain its central role in transcriptional activation. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale.

biochemistry↗

bioRxiv2024

Surface-Based vs. Voxel-Based Finite Element Head Models: Comparative Analyses of Strain Responses

Finite element (FE) models of the human head are important injury assessment tools but developing a high-quality, hexahedral-meshed FE head model without compromising geometric accuracy is a challenging task. Important brain features, such as the cortical folds and ventricles, were captured only in a handful of FE head models that were primarily developed from two meshing techniques, i.e., surface-based meshing with conforming elements to capture the interfacial boundaries and voxel-based meshing by converting the segmented voxels into elements with and without mesh smoothing. Despite these advancements, little knowledge existed of how similar the strain responses were between surface- and voxel-based FE head models. This study uniquely addressed this gap by presenting three anatomically detailed models - a surface-based model with conforming meshes to capture the cortical folds-subarachnoid cerebrospinal fluid and brain-ventricle interfaces, and two voxel-based models (with and without mesh smoothing) - derived from the same imaging dataset. All numerical settings in the three models were exactly the same, except for the meshes. These three models were employed to simulate head impacts. The results showed that, when calculating commonly used injury metrics, including the percentile strains below the maximum (e.g., 99 percentile strain) and the volume of brain element with the strain over certain thresholds, the responses of the three models were virtually identical. Different strain patterns existed between the surface- and the voxel-based models at the interfacial boundary (e.g., sulci and gyri in the cortex, regions adjacent to the falx and tentorium) with strain differences exceeding 0.1, but remarkable similarities were noted at the non-interfacial region. The mesh smoothing procedure marginally reduced the strain discrepancies between the voxel- and surface-based model. This study yielded new quantitative insights into the general similarity in the strain responses between the surface- and voxel-based FE head models and underscored that caution should be exercised when using the strain at the interface to predict injury.

bioengineering↗

bioRxiv2024

Organoid Modeling and Single-Cell Profiling Uncover the Migration Mechanism of Smooth Muscle Cells in Moyamoya Disease

Moyamoya disease (MMD) is a chronic cerebrovascular disorder characterized by progressive occlusion of the intracranial arteries, resulting in severe ischemic or hemorrhagic stroke. The main characteristic of the affected vessels in MMD is arterial intimal thickening. However, there are no in vitro or in vivo models that can mimic its vascular characteristics. Moreover, the mechanisms underlying the intimal thickening remain unexplained. Here, we generated vascular organoids by differentiating human induced pluripotent stem cell derived from the peripheral blood of MMD patients, thereby creating an organoid model reflecting both the genetic background and characteristics of the affected vessels. Through single-cell sequencing, we found the increased vascular smooth muscle cell (VSMC) proportion and its functional abnormalities in MMD organoids. Proteomics and RNA sequencing identified abnormal TUBA4A and TUBB4B overexpression in both the organoids and patient serum. The following in vitro experiments demonstrated that TUBA4A and TUBB4B promote the contractile-to-synthetic phenotypic switching, migration and proliferation in VSMC. Further experiments identified the GJA1-mediated PI3K/AKT/KLF4 pathway as a key regulating pathway of these phenotypic changes in VSMCs. Our findings demonstrate that the abnormal expression of TUBA4A and TUBB4B in VSMC might be a significant contributor to the intimal thickening in the affected vessels of MMD.

cell biology↗

bioRxiv2024

Prevalence of Problematic Papers in Non-Coding RNA Research

This study examines the prevalence of problematic papers in the rapidly growing field of non-coding RNA (ncRNA) research. Analysis of 153,826 ncRNA papers during 2000-2023 reveals that around 1.79% have been retracted and an additional 5.68% have raised concerns on PubPeer. The number of problematic papers has steadily increased, peaking in 2019 when the concerning and retraction rates reached nearly 10.8% and 3.7%, respectively. These unreliable papers have been widely disseminated, accumulating hundreds of thousands of citations in academic literature, patents, clinical trials, and policy documents, posing a significant threat to research integrity and public health. The main issues identified include image manipulation, data falsification, fake peer reviews, and ethical lapses. The findings call for urgent, comprehensive scrutiny of ncRNA publications and broader reforms to address systemic problems driving the proliferation of problematic research.

molecular biology↗

bioRxiv2024

Impact of intragenic NRXN1 deletions on early cortical development

BackgroundDeletions in NRXN1 are strongly associated with neurodevelopmental and psychiatric conditions. While exonic deletions are well-studied, intragenic deletions, particularly in intron 5, are less understood and generally consider benign. Recent studies show exonic deletions impact isoform diversity during neurodevelopment, affecting neurogenesis and neuronal function. However, whether intragenic deletions impact isoform expression and neurodevelopment remains underexplored. MethodsWe used hiPSCs from typically developing individuals (control) and those with NRXN1 intron 5 deletions to study neurodevelopment. HiPSCs were differentiated towards a cortical fate, with NRXN1 isoform expression, molecular differences, and neuronal morphology examined. ResultsWe observed distinct NRXN1 isoform expression dynamics during early neurodevelopment, with two expression peaks post-neuronal induction and NRXN1{beta} being most highly expressed. Both NRXN1 deletion and control lines showed similar acquisition of regional and cell fate identity, but significant differences in NRXN1 isoform expression were observed between deletion and control lines, and between deletion lines. RNA sequencing revealed genotype-dependent alterations, particularly in pathways related to synaptic function and neuronal morphology. Consistent with these findings, NRXN1 deletion lines exhibited altered dendrite outgrowth, with variations between deletion lines. ConclusionsOur results indicate a potential role for intron 5 in controlling NRXN1 isoform expression during neurodevelopment. Alterations in gene expression profiles, correlated with morphological changes, suggest a role for NRXN1 isoforms in shaping dendritic morphology. Molecular and cellular differences observed between lines with identical intronic deletions suggest that additional factors, such as genetic background or biological sex, may also play an important role in these phenotypes. Collectively, these findings indicate that NRXN1 intronic deletions are not benign, influencing isoform expression, cellular phenotypes, and neurodevelopment.

neuroscience↗

bioRxiv2024

Gut Microbiota and DTI Microstructural Brain Alterations in Rodents Due to Morphine Self-Administration

The opioid epidemic is an evolving health crisis in need of interventions that target all domains of maladaptive changes due to chronic use and abuse. Opioids are known for their effects on the opioid and dopaminergic systems, in addition to neurocircuitry changes that mediate changes in behavior; however, new research lines are looking at complementary changes in the brain and gut. The gut-brain axis (GBA) is a bidirectional signaling process that permits feedback between the brain and gut and is altered in subjects with opioid use disorders. In this work, we determine longitudinal, non-invasive, and in-vivo complementary changes in the brain and gut in rodents trained to self-administer morphine for two weeks using MRI and 16S rDNA analysis of fecal matter. We assess the changes occurring during both an acute phase (early in the self-administration process, after two days of self-administration) and a chronic phase (late in the self-administration process, after two weeks of self-administration), with all measurements benchmarked against baseline (naive, non-drug state). Rats were surgically implanted with an intravenous jugular catheter for self-administration of morphine. Rats were allowed to choose between an active lever, which delivers a single infusion of morphine (0.4 mg/kg/infusion), or an inactive lever, which had no consequence upon pressing. Animals were scanned in a 7T MRI scanner three times (baseline, acute, and chronic), and before scanning, fecal matter was collected from each rat. After the last scan session, a subset of animals was euthanized, and brains were preserved for immunohistochemistry analysis. We found early changes in gut microbiota diversity and specific abundance as early as the acute phase that persisted into the chronic phase. In MRI, we identified alterations in diffusivity indices both within subjects and between groups, showing a main effect in the striatum, thalamus, and somatosensory cortex. Finally, immunohistochemistry analyses revealed increased neuroinflammatory markers in the thalamus of rats exposed to morphine. Overall, we demonstrate that morphine self-administration shapes the brain and gut microbiota. In conclusion, gut changes precede the anatomical effects observed in MRI features, with neuroinflammation emerging as a crucial link mediating communication between the gut and the brain. This highlights neuroinflammation as a potential target in addressing the impacts of opioid use.

neuroscience↗