Biology subjects

Ahmed, A.

Publications and source records attributed to Ahmed, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Lipid Nanoparticle Delivery of Mesenchymal Stromal Cell-Derived microRNA 187-3p as a First-in-Class Therapy for Myocardial Dysfunction in Sepsis

BackgroundSepsis-induced myocardial dysfunction is a common and critical complication of sepsis. Extracellular vesicles (EVs) from clonally expanded immortalized mesenchymal stromal cells (ciMSCs) contain microRNAs that may be exploited as therapy. MethodsIn mouse models of septic cardiomyopathy induced by caecum ligation and puncture, cardiac function was determined by invasive and echocardiographic assessment. Primary cardiomyocytes derived from foetal murine and human adult ventricular tissue, as well as murine hearts were used for mechanistic studies. Studies using post-mortem human hearts or patient plasma, and clinical and echocardiographic measurements were used to establish translational relevance. ResultsIn preclinical models of sepsis, intravenous administration of either MSCs or ciMSC-EVs, given after the induction of sepsis, prevented a decrease in myocardial ejection fraction, ventricular inflammation, and mortality compared to placebo or platelet-derived control EVs. EV-microRNA sequencing identified enrichment for microRNA-187a-3p (miR-187) in ciMSC-EVs. miR-187 is anti-inflammatory; with interleukin-6 (IL-6) as its major target. Intravenous delivery of lipid nanoparticle (LNP) encapsulated miR-187 improved cardiac function, reduced inflammation, and enhanced survival of septic mice. In cardiomyocytes and in murine hearts, LNP-miR-187 reduces inflammation and expression of myocardial transcription factors linked to fetal gene reactivation in failing septic hearts. In human septic hearts, low circulating miR-187 levels correlate with reduced cardiac function and high sequential organ failure assessment (SOFA) scores. ConclusionThese findings support the development of first-in-class, cell-free, miRNA-based therapy as a novel approach to treat sepsis-induced cardiomyopathy to address a critical gap in sepsis care. One Sentence SummarymiR-based therapy for sepsis The Clinical PerspectiveA. What is NEW? Sepsis accounts for 1 in 5 deaths worldwide. Here, we demonstrate that sepsis-induced myocardial dysfunction represents a discrete, targetable sepsis-trait -- a distinct biological abnormality characterized by cardiomyocyte inflammation and fetal gene reactivation. This component contributes to the propagation of organ dysfunction and overall mortality and may respond to focused epigenetic-based interventions. B. What are the Clinical implications? Currently, there are no effective treatments to reduce, limit, or reverse the immune dysfunction component of sepsis that contributes to multiorgan failure, such as sepsis-induced cardiomyopathy. We identify miR-187 as a clinically relevant post-transcriptional regulator of cardiac inflammation and cardiomyocyte gene expression. Intravenous delivery of miR-187 encapsulated in a lipid nanoparticle (LNP) represents a fundamentally distinct, effective and pathogen-agnostic approach to correcting sepsis-induced cardiac dysfunction through modulation of cardiomyocyte inflammatory and metabolic pathways.

molecular biology↗

bioRxiv2025

Mapping the microRNA-mediated crosstalk between insulin resistance and Alzheimers disease : a computational genomic insight

Insulin resistance (IR) and Alzheimers disease (AD) share overlapping molecular mechanisms, but the precise link between these conditions remains unclear. MicroRNAs, as post-transcriptional regulators of gene expression, may mediate this connection by targeting genes involved in both pathways. In this study, we employed a multi-step bioinformatics approach to identify microRNAs that simultaneously regulate genes associated with IR and AD. Twenty key IR-related genes were selected from the literature, and their microRNA regulators were predicted using five computational tools. These predictions were validated using experimentally supported databases (TarBase and miRTarBase), and each miRNA-gene interaction was scored. Sixteen high-confidence microRNAs were shortlisted based on cumulative prediction and validation scores. These microRNAs were then analyzed for their interactions with AD pathway genes via KEGG pathway analysis. The AD-related target genes were further processed through protein-protein interaction network analysis using STRING and hub gene identification via Cytoscape. Functional enrichment of these hub genes using Gene Ontology and KEGG analysis revealed their involvement in shared biological processes, including apoptosis, insulin signaling, glucose metabolism, and neuroinflammation. Prominent candidates such as miR-7-5p, miR-106b, miR-424-5p, and miR-15a were identified. These results suggest that a subset of microRNAs may serve as critical molecular links between IR and AD, offering potential targets for early diagnosis and intervention.

neuroscience↗

bioRxiv2025

Alterations in Electroencephalography Signals in Female Fragile X Syndrome Mouse Model on a C57Bl/6J Background

BackgroundFragile X Syndrome (FXS), the most common monogenic cause of autism spectrum disorder, arises from FMR1 gene silencing and exhibits pronounced sex differences in prevalence and phenotypic severity. Electroencephalography (EEG) has emerged as a promising translational biomarker for FXS pathophysiology, yet prior research has predominantly focused on male cohorts. In the widely used C57Bl/6J (B6) mouse strain, male Fmr1 knockout (KO) models show increased absolute gamma power at both juvenile and adult stages, which may reflect cortical hyperexcitability. In contrast, little is known about female Fmr1 KO mice, except that they exhibit no gamma alterations in adulthood. This gap hinders understanding of sex-specific neurodevelopmental trajectories of EEG profile in FXS. Leveraging the genetic stability and translational relevance of the B6 strain, this study compares EEG profiles between juvenile female Fmr1 KO and wild-type (WT) B6 mice to address this critical gap. MethodsFrontal-parietal differential EEG was recorded in freely behaving mice using the Open-Source Electrophysiology Recording system for Rodents. Neural activity was analyzed across three recording conditions: in the home cage, light-dark arena, and open field arena. Computed metrics included absolute/relative power, peak alpha frequency, theta-beta ratio, phase-amplitude coupling, amplitude-amplitude coupling, and multiscale entropy to assess signal complexity. ResultsIn all recording conditions, Fmr1 KO mice exhibited reduced absolute power in theta, alpha, and beta frequency bands compared to WT controls. Relative power analysis revealed decreased alpha activity alongside increased gamma-band power, including both low and high gamma, in the KO mice. Cross-frequency coupling was disrupted, with diminished alpha-gamma phase-amplitude coupling. Amplitude-amplitude coupling between theta or alpha and gamma power displayed distinct changes in different recording conditions. Peak alpha frequency and theta-beta ratio were both reduced or unchanged in the KO mice, depending on the recording condition. Finally, EEG signal complexity remained comparable between the two genotypes across the conditions. Behaviorally, KO mice displayed hyper-exploration in the open field test, characterized by increased center time and entries. However, no overall robust correlations between EEG power in different frequency bands and behavioral parameters in the open field test were observed. Discussion and ConclusionOur results demonstrate that juvenile female Fmr1 KO mice on a B6 background exhibit EEG alterations highly consistent with those reported in FXS patients, particularly increased gamma and reduced alpha power. The robust increase in gamma activity reinforces its status as a reliable biomarker across preclinical and clinical studies, while alpha reductions and slowed peak alpha frequency implicate thalamocortical network involvement. Together, these findings highlight the translational value of this model for studying core circuit dysfunctions in FXS.

neuroscience↗

bioRxiv2025

Telomerase RNA gene duplications drive telomeric repeatdiversity and evolution in Andrena bees

Most organisms in the animal kingdom require a non-coding telomerease RNA (TR) in conjunction with the telomerase reverse transcriptase (TERT) to add telomere tandem repeats to chromosome ends to genomic instability. Recent studies reported an extensive diversity in the sequence of telomeric repeats in some insect species. Our investigation of TR genes in the Andrena genus provides convincing evidence for the presence of multiple TR gene copies with different template sequences for synthesis of distinct telomeric repeat sequences in several species. In this study we describe the structure, genomic coordinates and abundance of these TR genes, and correlate our findings with the levels of tandem repeats found in DNAseq data. Based on an analysis of the synthenic context of these newly predicted TR genes, we show evidence for the existence of multiple TR paralogs that diverged during the evolution of the genus Andrena. To our knowledge this is the first time such a phenomenon is observed in animals, although recently reported for plants. Interestingly, the comprehensive annotation of all TERT genes found in yet unannotated Andrena species shows no corresponding evolutionary changes in related TERT proteins encoded by a single copy gene. Our study suggests an evolutionary mechanism for diversification of telomeric repeat sequences in certain insect species through telomerase RNA gene duplication.

bioinformatics↗

bioRxiv2025

Beige fat appearance during lipoatrophy reveals trade-offs between metabolic homeostasis and female fertility

White adipose tissue (WAT) meets the energetic demands required for estrous cycle regularity, ovulation, and reproductive success in women. Here, we report WAT loss and subsequent female-specific compensatory beige fat recruitment impact metabolic and reproductive outcomes in mice. Female mice that undergo progressive lipoatrophy ( fat-less) displayed disrupted estrous cycles, reduced ovarian reserve, and subfertility. These effects were attributable to an accumulation of thermogenic beige fat cells in residual subcutaneous WAT depots and greater energy expenditure. Conversely, high-fat diet lowered energy expenditure and rescued estrous cycle regularity among fat-less mice compared to littermate controls, despite profound insulin resistance and metabolic dysfunction. Together, these findings provide evidence of trade-offs between the maintenance of metabolic homeostasis and reproduction, where increased energy expenditure and beige fat cell emergence compensate for fat loss but occur at the expense of fecundity in female mice.

cell biology↗

bioRxiv2025

CobVar - a comprehensive resource of Vitamin B 12-associated genomic variants

The importance of vitamin B12 (cobalamin) in numerous biological processes, including DNA synthesis and cellular energy production, underscores the need for therapeutic and public health strategies to address B12 insufficiency/deficiency in the population. Genetic variations in pathways influencing cobalamin absorption, transport, and metabolism can affect various direct and indirect measures of vitamin B12 status. To facilitate a structured approach to studying these genetic factors, we aimed to systematically curate and create a user-friendly web database that offers comprehensive data on genetic variants influencing B12 biomarkers. A Pubmed search was performed for 5 B12 traits (total serum/plasma B12, holotranscobalamin (active B12), total transcobalamin, holo haptocorrin, and methylmalonic acid) resulting in 493 research publications, of which 47 relevant publications were reviewed further. The database backend was built using MongoDB and the web interface was coded in PHP, JavaScript, HTML and CSS on an Apache HTTP server. We have manually curated and compiled the Cobalamin Associated Genetic Variant (CobVar) database, comprising a total of 324 genetic variant associations for 5 different vitamin B12 traits involving 222 unique genetic variants and 84 genes identified across several genome-wide association studies (GWAS) and candidate gene studies. About one-third of the total genetic variant associations have been reported in >1 independent studies and 15 variants in >1 ethnic group. FUT2 gene showed the maximum number of associations for total serum/plasma B12 (N=39), followed by MTHFR (N=24) and TCN2 (N=23). The database is accessible online at https://datatools.sjri.res.in/VBG/. CobVar is a vital resource for researchers and nutritionists, offering quick access to the latest developments in B12-related genetic variant research and serves as a valuable tool for advancing personalized treatment. Database URLhttps://datatools.sjri.res.in/VBG/.

genomics↗

bioRxiv2024

A microphysiological system of sterile injury demonstrates neutrophil reverse migration via macrophage-derived extracellular vesicle crosstalk.

Persistent neutrophilic inflammation can lead to tissue damage and chronic inflammation, contributing to non-healing wounds. The resolution phase of neutrophilic inflammation is critical to preventing tissue damage, as observed in diseases characterized by influx of neutrophils such as atherosclerosis and non-healing wounds. Animal models have provided insight into resolution of neutrophilic inflammation via efferocytosis and reverse migration (rM); however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for in vitro systems that can elucidate mechanisms of resolution of human neutrophilic inflammation. Here, we developed a human microphysiological system (MPS) to mimic an inflammatory sterile injury (SI) microenvironment to study the role of macrophage derived extracellular vesicles (M-EVs) in determining the resolution of inflammation via neutrophil rM. The MPS integrates a human umbilical vein endothelial cell (HUVEC) lined lumen, injury site spheroid, human neutrophils, macrophages and macrophage derived EVs to investigate the role of M-EVs in neutrophil rM in vitro. The key features of the MPS enabled us to demonstrate that EVs derived from macrophage subsets modulate migratory behavior in primary neutrophils differently in specific inflammatory microenvironments. Importantly, we identified a new mechanism underlying neutrophil rM via M-EV, where neutrophils exposed to M2-EV-derived IL-8 migrate away from the SI site upon reaching the site, using the SI MPS. Overall, our SI MPS system demonstrates a reverse migratory pattern in human primary neutrophils, advancing the study of the resolution of inflammation via M-EVs.

immunology↗

bioRxiv2024

Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification

PCR is a cornerstone of molecular biology, but many biologically important DNA templates remain difficult to amplify. Long tandem repeats, low-complexity tracts, and sequences with extreme base composition often yield low product levels, smeared bands, stutter products, or truncated amplicons. These failures can arise because repeated cycles of thermal denaturation and reannealing promote off-register annealing, polymerase slippage, secondary-structure formation, and incomplete extension. Previously, we developed SSB-Helicase Assisted Rapid PCR (SHARP), an isothermal amplification method in which an engineered superhelicase and single-stranded DNA-binding protein replace the thermal melting step of PCR with enzymatic strand separation. Here, we tested whether SHARP can improve amplification of templates that are refractory to conventional PCR. SHARP robustly amplified up to six identical tandem repeats of the Widom 601 nucleosome-positioning sequence and up to 35 identical ankyrin repeats, targets that were poorly amplified by conventional PCR under the conditions tested. SHARP also amplified templates with extreme base composition, including a 95% AT-rich template and GC-rich templates (up to ~95% GC), as well as a 99-repeat CGG tract associated with Fragile X syndrome and a CAG/CAA repeat tract from mutant HTT exon 1 associated with Huntington disease. Together, these results show that helicase-driven isothermal amplification can expand access to repetitive and compositionally extreme DNA sequences that are challenging for conventional thermocycling-based PCR.

bioengineering↗

bioRxiv2024

IgG autoantibodies in bullous pemphigoid directly induce a pathogenic MyD88-dependent pro-inflammatory response in keratinocytes:

AbstractWhile autoantibodies in bullous pemphigoid (BP) are known to activate the innate immune response, their direct effect on keratinocytes, and the contribution of BP-IgG autoantibody-dependent keratinocyte responses to BP pathology is largely unknown. Herein, we performed multiplex immunoassays and bulk RNA-seq on primary keratinocytes treated with IgG from BP patients or controls. We identified a pro-inflammatory and proteolytic response with release of several cytokines (IL-6, IL-24, TGF-{beta}1), chemokines (CXCL16, CTACK, MIP-3{beta}, RANTES), C1s, DPP4, and MMP-9. We further validated this response using spatial transcriptomics and scRNA-seq of diseased and control skin. Blistering itself appeared to be major driver of this inflammatory response, with attached BP skin and spongiotic dermatitis revealing highly similar transcriptomes. Based on elevated levels of MyD88 and MyD88-dependent cytokines, we studied the impact of MyD88 deficiency in keratinocytes and demonstrated that MyD88 regulates BP-IgG-induced expression of IL-8, IL-24, and MMP-9. Induction of experimental BP in mice with Krt14-specific Myd88 knockout revealed significantly decreased disease severity with decreased serum levels of IL-1{beta}, IL-4, and IL-9 indicating the contributory role of keratinocyte-derived skin inflammation towards systemic response. Our work demonstrates the key contributions of keratinocyte and MyD88 dependent signaling in response to autoantibodies in BP. Key Messages-IgG antibodies from bullous pemphigoid (BP) patients induce significant upregulation of several inflammatory markers in keratinocytes including cytokines (IL-6, IL-24, TGF-{beta}1), chemokines (CXCL16, CTACK, MIP-3{beta}, RANTES), C1s, DPP4, and MMP9. Several of these markers, including IL-8, IL-24, and MMP9 are regulated by MyD88. -Spatial transcriptomics reveals that BP patient blistered skin demonstrated similar transcriptomic profiles to BP-IgG-treated keratinocytes. With attached skin demonstrating a comparable transcriptome to that seen in spongiotic dermatitis. -In a mouse BP model, keratinocyte-specific MyD88 deficiency results in decreased disease severity with a subsequent decrease in serum IL-1{beta}, IL-4, and IL-9 levels. Capsule summaryIgG from patients with bullous pemphigoid (BP) induces a pro-inflammatory response in keratinocytes, indicating their direct role in driving the inflammatory response in BP.

immunology↗

bioRxiv2024

The mitochondrial dicarboxylate carrier mediates in vivo hepatic gluconeogenesis

Hepatic gluconeogenesis (GNG) is essential for maintaining euglycemia during prolonged fasting. However, GNG becomes pathologically elevated and drives chronic hyperglycemia in type 2 diabetes (T2D). Lactate/pyruvate is a major GNG substrate known to be imported into mitochondria for GNG. Yet, the subsequent mitochondrial carbon export mechanisms required to supply the extra-mitochondrial canonical GNG pathway have not been genetically delineated. Here, we evaluated the role of the mitochondrial dicarboxylate carrier (DiC) in mediating GNG from lactate/pyruvate. We generated liver-specific DiC knockout (DiC LivKO) mice. During lactate/pyruvate tolerance tests, DiC LivKO decreased plasma glucose excursion and 13C-lactate/-pyruvate flux into hepatic and plasma glucose. In a Western diet (WD) feeding model of T2D, acute DiC LivKO after induction of obesity decreased lactate/pyruvate-driven GNG, hyperglycemia, and hyperinsulinemia. Our results show that mitochondrial carbon export through the DiC mediates GNG and that the DiC contributes to impaired glucose homeostasis in a mouse model of T2D.

biochemistry↗

bioRxiv2024

JAK2/STAT3 signaling pathway mediates methylmercury toxicity in mouse astrocyte neuronal C8-D1A cell line

Methylmercury (MeHg) is an environmental pollutant. Consumption of contaminated fish is the main exposure route in humans, leading to severe neurological disorders. Upon ingestion MeHg reaches the brain and selectively accumulates in astrocytes disrupting glutamate and calcium homeostasis and increasing oxidative stress. Despite extensive research, the molecular mechanisms underlying MeHg neurotoxicity remain incompletely understood. The induction of nuclear factor erythroid 2-related factor 2 (Nrf2) and its role activating antioxidant responses during MeHg-induced oxidative injury have garnered significant attention as a potential therapeutic target against MeHg toxicity. However, recent studies indicate that the Nrf2 signaling pathway alone may not be sufficient to mitigate MeHg-induced damage, suggesting the existence of other protective mechanisms. The signal transducer and activator of transcription 3 (STAT3) plays a crucial role in cell growth and survival. Several studies have also highlighted its involvement in regulating redox homeostasis, thereby preventing oxidative stress through mechanisms that involve modulation of nuclear genes that encode electron transport complexes (ETC) and antioxidant enzymes. These characteristics suggest that STAT3 could serve as a viable mechanism to mitigate MeHg toxicity, either in conjunction with or as an alternative to Nrf2 signaling. Our previous findings demonstrated that MeHg activates the STAT3 signaling pathway in the GT1-7 hypothalamic neuronal cell line, suggesting its potential role in promoting neuroprotection. Here, to elucidate the role of the STAT3 signaling pathway in MeHg neurotoxicity, we pharmacologically inhibited STAT3 using AG490 in the C8D1A astrocytic cell line exposed to 10 {micro}M MeHg. Our data demonstrated that pharmacological inhibition of STAT3 phosphorylation exacerbates MeHg-induced mortality, antioxidant responses, and ROS production, suggesting that STAT3 may contribute to neuroprotection against MeHg exposure in astrocytes.

pharmacology and toxicology↗

bioRxiv2024

An in vivo 'turning model' reveals new RanBP9 interactions in lung macrophages.

The biological functions of the scaffold protein Ran Binding Protein 9 (RanBP9) remain elusive in macrophages or any other cell type where this protein is expressed together with its CTLH (C-terminal to LisH) complex partners. We have engineered a new mouse model, named RanBP9-TurnX, where RanBP9 fused to three copies of the HA tag (RanBP9-3xHA) can be turned into RanBP9-V5 tagged upon Cre-mediated recombination. We created this model to enable stringent biochemical studies at cell type specific level throughout the entire organism. Here, we have used this tool crossed with LysM-Cre transgenic mice to identify RanBP9 interactions in lung macrophages. We show that RanBP9-V5 and RanBP9-3xHA can be both co-immunoprecipitated with the known members of the CTLH complex from the same whole lung lysates. However, more than ninety percent of the proteins pulled down by RanBP9-V5 differ from those pulled-down by RanBP9-HA. The lung RanBP9-V5 associated proteome includes previously unknown interactions with macrophage-specific proteins as well as with players of the innate immune response, DNA damage response, metabolism, and mitochondrial function. This work provides the first lung specific RanBP9-associated interactome in physiological conditions and reveals that RanBP9 and the CTLH complex could be key regulators of macrophage bioenergetics and immune functions.

cell biology↗

bioRxiv2024

HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA+ plasma cells in the GI tract

Gastrointestinal (GI) B cells and plasma cells (PCs) are critical to mucosal homeostasis and the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs sampled from the colon and ileum during both viremic and suppressed HIV-1 infection identified a reduction in germinal center (GC) B cells and follicular dendritic cells (FDCs) during HIV-1 viremia. IgA+ PCs are the major cellular output of intestinal GCs and were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling, persisted in antiretroviral therapy (ART)-treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations were associated with changes in the intestinal microbiome composition and systemic inflammation. These findings highlight a key immune defect in the GI mucosa due to HIV-1 viremia. One Sentence SummaryIntestinal germinal center B cell reduction in HIV-1 infection linked to reduced IgA+ plasma cells and systemic inflammation.

immunology↗

bioRxiv2024

Changes in Electroencephalography signals in a juvenile female Fragile X Syndrome mouse model

BackgroundFragile X syndrome (FXS) is the leading monogenic cause of Autism. No broadly effective support option currently exists for FXS, and drug development has suffered many failures in clinical trials based on promising preclinical findings. Thus, effective translational biomarkers of treatment outcomes are needed. Recently, electroencephalography (EEG) has been proposed as a translational biomarker in FXS. Recent years have seen an exciting emergence of novel EEG signal analyses from FXS patients. However, there is a notable gap in corresponding analyses conducted on animal models of the disorder. Being X-linked, FXS is more prevalent in males than females, and there exist significant phenotype differences between males and females with FXS. Recent studies involving male FXS participants and rodent models have identified an increase in absolute gamma EEG power, while alpha power is found to be either decreased or unchanged. However, there is not enough research on female FXS patients or models. In addition, studying EEG activity in both young and adult FXS patients or rodent models is crucial for better understanding of the disorders effects on brain development. Therefore, using the well established fmr1 knockout (KO) mouse model of FXS, we aim to compare EEG signal between female wild-type (WT) and female model mice at both juvenile and adult ages. MethodsFrontal-parietal differential EEG was recorded using a stand-alone Open-Source Electrophysiology Recording system for Rodents (OSERR). EEG activity was recorded in three different conditions: a) in the subjects home cage, and in the arenas for b) light -dark test and c) open field test. Absolute and relative EEG power as well as peak alpha frequency, theta-beta ratio, phase-amplitude and amplitude-amplitude coupling, and EEG signal complexity were computed for each condition. ResultsIn our study, we found absolute alpha, beta, gamma and total EEG power is increased in the female model compared to WT controls at the juvenile and adult ages. Alongside, relative theta power is decreased in the model. Additionally, phase-amplitude and amplitude-amplitude coupling is altered in the model. Furthermore, peak alpha frequency is increase, and theta-beta ratio is decreased in the model. Lastly, no change in EEG signal complexity is found. Discussion and ConclusionConsistent with most findings from FXS patients and rodent models, our results demonstrated an increase in gamma power in fmr1KO female mice, reinforcing gamma power as a robust and reliable EEG phenotype across FXS models. Additionally, theta-gamma cross frequency amplitude coupling is inversely coupled in female FXS model, which is similar to what has been reported in FXS patients. Overall, our findings reveal that not all EEG biomarkers observed in FXS patients are replicated in the female FXS model. For example, peak alpha frequency, theta-beta ratio, and brain signal complexity showed discrepancies between the mouse models and FXS patients. Additionally, when compared to previously reported EEG changes in male FXS mouse models, our results highlight the presence of a potential sex-based difference in EEG phenotypes at both juvenile and adult stages of fmr1 KO mouse models. Together, our study indicates that certain EEG parameters may be more translatable between rodent models and FXS patients than others and underscore the importance of considering sex and developmental stage as a critical factor when using EEG as a biomarker in FXS research.

neuroscience↗

bioRxiv2024

Exploring the Dynamics of Social Interactions During the Juvenile Stage in a Mouse Model of Fragile X Syndrome

IntroductionFragile X Syndrome (FXS), caused by Fmr1 mutations, is linked to cognitive and behavioral differences, including altered social interactions. Most mouse studies focus on adults, despite human research showing critical developmental changes in childhood and adolescence. We examined social behavior in juvenile male and female Fmr1 knockout (KO) mice as well as heterozygous (HET) females. We further assessed cortical activity in KO females to better understand early phenotypes. MethodsJuvenile mice of both sexes and genotypes were paired in same-sex, novel dyads for 10-minute interactions. Key social behaviors such as head, anogenital, and body sniffing, and physical touch, as well as distance travelled, were analyzed with a marker-less tracking software. Frontal-parietal EEG recordings were collected from wild-type (WT) and KO females in home cage and social contexts to analyze power spectra across frequency bands. ResultsHET and KO females engaged in more frequent but shorter interaction events compared to WT females, with HET females showing the highest counts. Males displayed similar trends when comparing KO and WT. Males engaged in overall higher interaction events than females. EEG analyses revealed altered oscillatory activity in KO females compared to WT females, especially within theta, alpha, and beta bands, most prominently during the early interaction phase. Locomotor activity correlated weakly with head/anogenital sniffing but more strongly with body sniffing and touch. DiscussionThese findings suggest that Fmr1-related differences in juvenile social behavior are sex-dependent and associated with cortical oscillatory changes. Characterizing these early phenotypes in both sexes allows us to further understand FXS development and informs potential routes for early intervention. Key PointsO_LIFragile X Syndrome (FXS), the leading inherited cause of autism, is associated with disruptions in social behavior. C_LIO_LIWhile social phenotypes are relatively well described in adult mouse models of FXS, juvenile manifestations remain poorly understood. C_LIO_LISocial behavior was assessed in juvenile male and female Fmr1 knockout (KO), heterozygous (HET, female only), and wildtype (WT) mice, and frontal-parietal EEG recordings were collected from WT and KO females. C_LIO_LIHET and KO females exhibited more frequent but shorter social interactions than WT females, with HET showing the greatest number of events. Males showed similar patterns when comparing KO and WT. Males engaged in higher overall interaction events than females. EEG recordings revealed altered oscillatory activity in KO compared to WT females, most pronounced during the early phase of social encounter. C_LIO_LIThese findings reveal sex- and genotype-dependent differences in juvenile social behavior and cortical activity, highlighting the importance of studying juvenile development in FXS. C_LI

animal behavior and cognition↗

bioRxiv2024

A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

O_LIWhite oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. C_LIO_LIWe report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. C_LIO_LIOur genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus. Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). C_LIO_LIThe white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade. C_LI

genomics↗

bioRxiv2024

Unravelling the conundrum of nucleolar NR2F1 localization: A comparative analysis of NR2F1 antibody-based approaches in vitro and in vivo.

As a transcription factor, NR2F1 regulates spatiotemporal gene expression during development and in adulthood. Aberrant NR2F1 causes a rare neurodevelopmental disorder known as Bosch-Boonstra- Schaaf Optic Atrophy Syndrome. In addition, altered NR2F1 expression is frequently observed in various cancers and is considered a prognostic marker or potential therapeutic target. In this context, NR2F1 has been shown to localize not only in the nucleus but also in the nucleoli, suggesting a novel non-canonical role in this compartment. Hence, we studied this phenomenon employing various in vitro and in vivo models in different antibody-dependent approaches. Examination of seven commonly used anti-NR2F1 antibodies in different human cancer and stem cells as well as in wild type and null mice revealed that the nucleolar localization of NR2F1 is artificial and does not play a functional role. Our subsequent comparative analysis demonstrated for the first time which anti-NR2F1 antibody best fits which approach. As our data allow for correct data interpretation, making them publicly available may have far-reaching implications for NR2F1 research in health and disease. More generally, the study also underlines the need to optimize any antibody-mediated technique.

cell biology↗

bioRxiv2023

Generation and characterization of a novel mouse model of Becker Muscular Dystrophy with a deletion of exons 52 to 55

Becker Muscular Dystrophy (BMD) is a rare X-linked recessive neuromuscular disorder caused by in-frame deletions in the DMD gene that result in the production of a truncated, yet functional, dystrophin protein. BMD is often considered a milder form of Duchenne Muscular Dystrophy, in which mutations typically result in the disruption of the reading frame and the malfunction or loss of dystrophin. The consequences of BMD-causing in-frame deletions on the organism are more difficult to predict, especially in regard to long-term prognosis. Here, we employed CRISPR-Cas9 technology to generate a new Dmd del52-55 mouse model by deleting exons 52-55, resulting in a typical BMD-like in-frame deletion. To delineate the long-term effects of this deletion, we studied these mice over 52 weeks. Our results suggest that a truncated dystrophin is sufficient to maintain wildtype-like muscle and heart functions in young mice. However, the truncated protein appears insufficient to maintain normal muscle homeostasis and protect against exercise-induced damage at 52 weeks. To further delineate the effects of the exons 52-55 in-frame deletion, we performed RNA-Seq pre- and post-exercise and identified several differentially expressed pathways that could explain the abnormal muscle phenotype observed at 52 weeks in the BMD model. Summary StatementWe generated and characterized the long-term effects of a Becker Muscular Dystrophy-like in-frame deletion of exon 52 to 55 in mice.

genetics↗