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Cheng, N.

Publications and source records attributed to Cheng, N..

At least 19 recordsLinked to original sources

Altered stimulus-specific adaptation at the auditory cortex of a mouse model of Fragile X Syndrome

Auditory hypersensitivity or decreased sound tolerance is a common phenotype of Fragile X Syndrome (FXS). Impairments in adaptation, defined as the reduction in the neuronal responsiveness to repeating sounds, can contribute to this prevalent phenotype. Previous studies on event-related potential observed impairments in mismatch negativity (MMN) in both FXS individuals and in the FMR1-knockout (KO) mouse model of FXS. Therefore, in the present study we characterized stimulus-specific adaptation (SSA), a neural correlate of MMN, at the auditory cortex (AC) of anesthetized (with ketamine/xylazine) female and male postnatal day 20 (P20) wild-type (WT) and FMR1-KO mice, using the oddball paradigm with either 4 Hz or 1 Hz repetition rate. We observed robust SSA at the 4 Hz repetition rate of the oddball paradigm in the AC neurons of all four groups of animals. We also noted that the strength of SSA diminished between 4 to 1 Hz repetition rate. In addition, at both the 4 Hz and 1 Hz repetition rate, reduced SSA was observed particularly in the male FMR1-KO mice compared to their WT counterparts, while female WT and FMR1-KO mice displayed similar SSA. In terms of sex differences, male FMR1-KO mice had lower SSA than female FMR1-KO mice, while SSA was similar in male and female WT mice. Overall, our observation of reduced SSA in the male FMR1-KO mice suggests that impairments in neuronal adaptation potentially contribute to the auditory hypersensitivity phenotype particularly within the male population.

neuroscience↗

Enrichment of methylated cell-free placental DNA

Abstract. Introduction: Preterm birth drives adverse perinatal maternal and infant health outcomes through heterogeneous symptoms, severity, and etiologies. Delivery prior to reaching 37 weeks of gestation may result from medically indicated intervention for pregnancy complications or spontaneously in the absence of prior symptoms. Placental tissue collected following preterm birth exhibits differential DNA methylation compared to full-term placentas and may indicate pregnancy health during gestation. Placental DNA currently has limited utility for assessing health of ongoing pregnancy, as sampling placental tissue during gestation increases the risk of infection and miscarriage. Risks associated with placental sampling during pregnancy limit the use of DNA methylation in clinical preterm birth prediction. Assessing preterm birth risk during gestation requires non-invasive methods for characterizing placental DNA methylation. Results: We quantified genome-wide DNA methylation patterns of hypermethylated cell-free DNA in pregnant (n = 99) and non-pregnant (n = 93) plasma using cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq). In each sample, we assessed DNA methylation status in 300-bp genomic windows, examining both sequencing read counts and calculated absolute molar DNA amount. Known hypermethylated placental regions, including RASSF1, STAT5A, and ERG promoters showed significantly increased odds of detection in pregnant samples, suggesting enrichment of cell-free placental DNA. Of the 536,444 300-bp windows examined, 173,071 (32%) showed significant enrichment in pregnant plasma. Linear modeling identified 107,505 differentially methylated regions (DMRs) associated with pregnancies later diagnosed with intrauterine growth restriction (IUGR) (n = 22). Alu elements showed increased representation in these DMRs than expected, while other repetitive elements exhibited underrepresentation. Discussion: These results demonstrate cfMeDIP-seq's ability to enrich for cell-free placental DNA and characterize cell-free DNA methylation signatures of pregnancies complicated by IUGR. Enrichment of cell-free placental DNA enables non-invasive profiling of placental DNA methylation from maternal plasma. Detectable epigenetic signatures in maternal plasma may identify pregnancies at elevated risk for preterm birth before clinical symptoms appear. Our findings further highlight the potential of cell-free placental DNA for monitoring pregnancy health.

genomics↗

Omics-scale capture of electrophilic metabolites

The majority of metabolic pathways rely on the production of activated electrophilic intermediates, e.g., coenzyme-A esters, and their chemical structures and abundances are central to understanding enzyme function and biochemical mechanisms. However, most electrophilic metabolites are lost in traditional metabolomic analysis and thus remain poorly characterized. Here we introduce a biochemical probe, O-(trimethylammoniobutyl)-hydroxylamine (TAMOHA), that enables comprehensive profiling of electrophilic species such as coenzyme-A esters, ketones, and aldehydes. TAMOHA incorporates a highly nucleophilic hydroxyl amine that reacts quickly with electrophilic species upon tissue lysis, trapping them as stable derivatives that feature a tetraalkylammonium moiety whose constitutive charge and characteristic MS2 fragmentation fingerprint enable their highly sensitive detection. Using TAMOHA to survey the electrophilomes of E. coli, C. elegans, and mouse revealed several thousand electrophilic metabolites, most of which have not been characterized. We then demonstrate trapping of electrophilic metabolites with TAMOHA in the context of specific biochemical pathways, confirming previously proposed functions of two fatty acid metabolism enzymes, detecting formaldehyde production in mice, and providing new insights into the biosynthesis of ascaroside pheromones in C. elegans. We anticipate that use of TAMOHA for the profiling of electrophilic species will help clarify enzyme function and uncover previously elusive biochemical mechanisms in a wide range of biological systems. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/743530v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@79a416org.highwire.dtl.DTLVardef@3b937org.highwire.dtl.DTLVardef@74cae9org.highwire.dtl.DTLVardef@1b5a915_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

LZTS2 Emerges as a Regulator of Craniofacial Development and Modulator of DYRK1A

BackgroundPrecise control of DYRK1A dosage is essential for embryonic development, including craniofacial morphogenesis. While LZTS2 is among the most consistently identified DYRK1A-interacting proteins, its roles in embryonic development remain incompletely understood, and its potential contribution to craniofacial development has not been examined. Xenopus laevis was used to test the role of LZTS2 in craniofacial development and its functional relationship with DYRK1A. ResultsLzts2 and Dyrk1a showed overlapping expression during craniofacial development, with both proteins present in developing facial tissues. Knockdown of Lzts2 disrupted craniofacial morphogenesis and reduced expression of the neural crest-associated genes sox9 and pax3. These phenotypes closely resembled those caused by decreasing Dyrk1a function. Sub-phenotypic reductions of Lzts2 and Dyrk1a synergized to produce craniofacial defects, while partial reduction of Lzts2 attenuated aspects of the phenotype caused by Dyrk1a overexpression. Comparative analysis of human phenotypes associated with copy number gains of LZTS2 and DYRK1A revealed striking overlap, consistent with a potential functional interaction between these genes in humans. ConclusionsThese findings identify Lzts2 as a previously unrecognized regulator of craniofacial development and support a functional interaction with Dyrk1a during embryogenesis. Modulating LZTS2 or related regulatory partners may provide a strategy to selectively tune DYRK1A-dependent developmental pathways

developmental biology↗

Changes in perineuronal net and parvalbumin expression in the orbitofrontal cortex of male Wistar rats following repeated fentanyl administration

The misuse of opioid medications is a significant health issue in the United States. Very few studies have investigated the effect of opioids on perineuronal nets (PNNs), scaffold-like structures that surround neurons and are involved in the regulation of plasticity-dependent mechanisms such as development, learning and memory, and acquisition of addiction-like phenotypes. Regulation of PNNs in the orbitofrontal cortex (OFC) during periods of drug intoxication or withdrawal is widely unknown. In this study, male Wistar rats were injected with fentanyl (0.125 mg/kg, s.c.) or 0.9% saline twice daily for 7 days and once on day 8 (7continuous days following by 3 days of abstinence) or twice daily for 15 days (5 continuous days followed by 2 days of abstinence for more than 3 weeks) and twice on day 16. Antinociception was evaluated using the tail immersion test immediately before and 30 minutes after injections. Whole-brain coronal slices were collected, and immunohistochemistry was used to identify Wisteria Floribunda Agglutinin (WFA)-positive PNNs and parvalbumin (PV)-expressing cells. Results confirmed that repeated fentanyl injections induced tolerance to the antinociceptive effects, which normalized following acute abstinence periods. WFA intensity decreased following 8 days of injections. Analyses confirmed significant correlations between PV+ density and tail withdrawal latency following 8 days of fentanyl injections. These data confirm that repeated fentanyl injections modulate both WFA+ and PV+ expression in the rodent brain and antinociceptive tolerance in a duration-dependent manner. Overall, these data suggest that perineuronal nets may mediate opioid-induced behavioral effects, such as antinociceptive tolerance, following repeated administration and abstinence in rats.

neuroscience↗

The role of Fragile X in the control of vertebrate spinal cord networks

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and the leading monogenic cause of autism, resulting from mutations in the Fmr1 gene. While extensive research points to widespread circuit hyperexcitability across cortical and subcortical circuits, the contribution of the spinal cord circuits in the motor phenotypes associated with FXS remains largely unexplored. Given that Fmr1 is expressed in both dorsal and ventral spinal cord, including motoneurons, the possibility exists that loss of its protein product, FMRP, disrupts locomotor circuitry. Here, we investigate whether Fmr1 deletion alters the function of the spinal central pattern generator (CPG) networks and gait-related motor output. Using isolated neonatal spinal cord preparations from Fmr1 knockout (Fmr1 KO) mice, we assessed the ability of spinal circuits to generate coordinated fictive locomotor activity in vitro. In parallel, we quantified the gait parameters and motor performance in freely moving adult mice during unskilled and skill-demanding tasks. Our findings indicate that, despite the absence of FMRP in spinal neurons, neonatal Fmr1 KO spinal cords generated robust and coordinated locomotor rhythms compared to controls. Consistently, adult Fmr1 KO mice exhibited normal gait metrics under baseline conditions. However, these mice displayed hyperactivity and performance deficits during more challenging motor tasks demanding higher coordination. These findings suggest that the fundamental locomotor circuitry is preserved in FXS, likely through compensatory mechanisms. Consequently, motor impairments in FXS may arise primarily from supraspinal or integrative circuit dysfunction, rather than intrinsic deficits in spinal CPG function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/704392v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@19a64cborg.highwire.dtl.DTLVardef@14f8ad2org.highwire.dtl.DTLVardef@1230cbforg.highwire.dtl.DTLVardef@19fd51_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINeonatal Fmr1 KO spinal cords generated robust, coordinated locomotor rhythms similar to controls. C_LIO_LIAdult Fmr1 KO mice exhibited normal gait metrics during baseline, unskilled locomotion. C_LIO_LIFmr1 KO mice displayed hyperactivity and performance deficits during skill-demanding motor tasks. C_LIO_LIFXS motor impairments may arise primarily from supraspinal or integrative circuit dysfunction C_LIO_LISpinal cord circuitry appears to compensate for the fundamental loss of Fmr1 function. C_LI

neuroscience↗

Context-aware Multi-Property Antibody Predictor: a Novel Framework Integrating Text and Protein Language Models

Recent advances in Machine Learning have transformed antibody development through in-silico models, accelerating therapeutic candidate identification. However, challenges persist: rapid adaptation of property predictors to laboratory-specific assays with incomplete datasets; batch effects introducing systematic bias; assay costs necessitating efficient unseen property prediction. We introduce a novel multi-modal architecture featuring specialized tokenization and embedding projection that integrates text and protein language models (pLM) and a learning strategy to enable in-context learning for multi-property prediction without learning shortcuts. Our framework enables prompting without dictionary merging across modalities, creating a compact model capable of in-context learning for multi-property prediction. The orchestrating model avoids pLM-to-text projection while enabling inference-time adaptation without retraining. Using 876,898 antibodies with batch effect simulation, our architecture achieved Spearmans {rho}>0.8 across multiple developability properties, significantly outperforming fine-tuned multimodal-LLMs and showed the ability of leveraging correlation between properties for prediction. This approach has the potential to address critical antibody development challenges.

bioinformatics↗

Umbilical cord structure shapes feto-maternal heat exchange across mammals

The umbilical cord exhibits striking structural diversity across placental mammals; however, the consequences of such variation on physiological function are poorly understood. Combining comparative anatomy across 130 mammal species with ancestral-trait reconstruction, multimodal imaging, and physics-based transport modelling, we show that the human umbilical cord structure is uncommon in other mammals and that the ancestral umbilical cord was unspiralled, with three vessels and an allantoic duct. Across species, vessel number and cord length correlate with birth weight: four-vessel cords and the persistence of an allantoic duct occur in species with heavier neonates, while two-vessel cords are confined to small muroid rodents. Mathematical modelling predicts that oxygen delivery remains near maximal across all cord architectures, but placental heat removal depends strongly on umbilical flow, and moderately on cord length and coiling. Scaling of umbilical flow with birth weight implies that larger species approach near-maximal heat-removal capacity, while smaller species are less efficient. Finally, three-dimensional imaging of the human cord reveals a triple-helix configuration of umbilical vessels, rather than arteries simply twisting around a central vein. This, and other observed cross-sectional vessel configurations in mammals and atypical human cords, aligns with theoretically predicted arrangements that minimize inter-vessel shunting, supporting an adaptive role for cord geometry in thermal regulation function. Together, these findings reframe the umbilical cord as a heat-exchange system and link its structural diversity to evolutionary history, neonatal mass, and maternal investment, with implications for fetal resilience to environmental stress.

physiology↗

PlantScience.ai: An LLM-Powered Virtual Scientist for Plant Science

The accelerating growth of plant science literature presents a major challenge for researchers seeking to extract accurate, up-to-date knowledge from an increasingly fragmented and domain-specific corpus. General-purpose large language models (LLMs), while powerful, often misinterpret plant science terminology and lack mechanisms for source traceability. We created PlantScience.ai, a virtual plant biology scientist powered by our automated scientific knowledge graph construction pipeline (AutoSKG). PlantScience.ai exhibits expert-level reasoning in plant biology and maintains scholarly rigour in its citations. Through continuous learning, it integrates the latest research, ensuring that its knowledge base remains current and scientifically robust. Apart from providing the answers to the scientific questions, PlantScience.ai can interact with human scientists, follow instructions, and retrieve information with citation awareness, grounding each response in primary sources to ensure accuracy and verifiability. PlantScience.ai marks a pivotal advance toward a collaborative scientific paradigm in which virtual and human plant scientists work synergistically to accelerate discovery while preserving the unique value of human insight. PlantScience.ai is available at https://plantscience.ai.

plant biology↗

Early developmental characterization of gap-induced prepulse inhibition and habituation in the Fragile X Syndrome mouse model

IntroductionAtypical sensory processing, particularly auditory hypersensitivity, is a common and debilitating phenotype of Fragile X Syndrome (FXS). Electrophysiology studies in FMR1-knockout (KO) mice previously observed hyperexcitability at the auditory cortex (AC), with enhanced neuronal firing to auditory stimuli. Prepulse inhibition (PPI), a behavioral measure of sensorimotor gating, is robustly impaired in FXS individuals. Interestingly, a related paradigm called gap-induced inhibition of the acoustic startle (GPIAS) is mediated by the AC, and a previous study observed decreased GPIAS in mature FMR1-KO mice. Further, habituation is also an important sensory filtering mechanism, which has been reported to be impaired in mature FMR1-KO mice. However, not much is known about GPIAS and habituation in FMR1- KO mice during early development. MethodsWe evaluated GPIAS in male and female FMR1-KO mice at post-natal days 15 (P15), 20 (P20) and 30 (P30). The paradigm consisted of a prepulse stimulus (a gap in a continuous background noise) followed by a startle stimulus, with an inter-stimulus interval of 50 or 100 ms. Habituation was assessed prior to the GPIAS trials, with a series of startle only stimulus. ResultsWe observed a trend for genotype difference in acoustic startle response (ASR) magnitude, particularly in the female mice at P30. No significant genotype differences were noted in GPIAS or latency of ASR. Response duration was significantly increased in the male FMR1-KO mice compared to their WT counterparts during early development. Significant genotype differences were also observed in habituation and sensitization. In terms of development, we observed a significant increase in GPIAS with maturation. Furthermore, we also observed significant changes in the magnitude, response latency and duration of ASR with maturation. Finally, significant sex differences were observed in ASR magnitude and duration. ConclusionOur findings suggest that behavioral responses to auditory stimuli are dynamic during development and differ between females and males, an important consideration for future study design. Additionally, the FMR1-KO mice display habituation deficits during early development, which could be an ideal window for addressing auditory hypersensitivity in FXS.

neuroscience↗

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↗

Structural Identification of Major Molecular Determinants for Phosphotyrosine Recognition in Tyrosine Kinases Reveals Tumour Promoting and Suppressive Functions

Protein tyrosine kinases activate signaling pathways by catalyzing the phosphorylation of tyrosine residues in their substrates. Mounting evidence suggests that, in addition to recognizing phosphorylated tyrosine (pTyr) residues through specific phosphobinding modules, many protein kinases selectively recognize pTyr directly adjacent to the tyrosine residue they phosphorylate and catalyze the formation of twin pTyr-pTyr sites. Here, we demonstrate the importance of this phosphopriming-driven twin pTyr signaling in promoting cell cycle progression through the cell cycle-inhibitory protein p27Kip1. We identify, structurally resolve, and tune two distinct molecular determinants driving the selective recognition of pTyr directly N- and C-terminal to the target phospho-acceptor tyrosine site. We further show structural and biochemical conservation in this recognition, and identify cancer-associated alterations to these determinants that are unable to recognize phosphoprimed substrates. Finally, using an in vivo mouse model of leukemia we show that Bcr-Abl mutants unable to recognize phosphoprimed substrates paradoxically result in enhanced tumor development and progression. These data indicate that Bcr-Abl, like other proto-oncogenes such as Ras or Myc, engages both pro- and anti-oncogenic programs - but in the case of Bcr-Abl, this is accomplished through a mechanism involving traditional and phosphoprimed substrate recognition.

biochemistry↗

Alterations in auditory midbrain processing is observed in both female andmale mouse model of Fragile X Syndrome

IntroductionSensory processing deficits presenting as auditory hypersensitivity is a common phenotype associated with Fragile X Syndrome (FXS), a leading monogenic cause of intellectual disability and autism spectrum disorder. Auditory hypersensitivity can also be observed in the FMR1-knockout (KO) mice, a well-established mouse model of autism and FXS. FXS is an X-linked disorder that is more prevalent in males compared to females, as a result most auditory and electrophysiology studies are performed in males. Previous in-vivo electrophysiology studies at the inferior colliculus (IC), an essential component of the auditory pathway, in male FMR1-KO mice at post-natal days 14, 21 and 34 (P14, P21 and P34) demonstrated increased neuronal firing, suggesting that the IC could play a role in auditory hypersensitivity. However, very little is known about the role of the central nucleus of the IC (ICc) and auditory hypersensitivity in females. MethodsHere we investigated auditory processing at P20 and P30, representative of early and late developmental stage of auditory development, respectively, at the central nucleus of the IC (ICc) of both female and male FMR1-KO mice, compared with wildtype (WT) animals. ResultsIn-vivo electrophysiology recordings from the ICc neurons of the FMR1-KO mice at both developmental ages demonstrated increased response magnitude measured by spike number to pure tones of varying frequency and amplitude, compared with age- and sex-matched WT animals. In addition, within the FMR1-KO group we also observed significant developmental and sex difference wherein higher response magnitudes were displayed at P20 and in the female mice. Minimum threshold of ICc neuron in the KO mice was significantly decreased at both P20 and P30. The ICc neurons in the KO mice also displayed increased response duration compared to WT animals at both P20 and P30, but significant sex difference was only observed at P30. Our data also indicated that the ICc neurons of both groups displayed weak negative relationship between latency and response magnitude at P20, and at P30 the WT mice showed a stronger relationship only in the female group. In terms of developmental changes, we observed decreasing neuronal firing only in the KO mice between 20- and 30-day old female and male mice. Reduced response duration was observed in 30-day old mice of both sexes of both genotypes. Regarding minimum threshold, we observed a decline between early and late auditory development only in the male mice. Finally, our results also indicated that in the WT mice the reverse relationship between latency and response magnitude became more pronounced and consistent with age, a developmental trend that was absent in both the female and male FMR1-KO mice. DiscussionOverall, our findings demonstrate that auditory processing deficits can also be observed in the female FMR1-KO mice using in-vivo electrophysiology studies, highlighting the importance of including female subjects in future studies. These results also indicate that auditory hypersensitivity can be observed robustly in younger mice, suggesting that the early development stage could be an ideal target for interventions.

neuroscience↗

Pervanadate-induced oxidation relieves autoinhibition of SRC protein tyrosine kinase

Dynamic regulation of protein tyrosine phosphorylation (pTyr) by phosphatases (PTPs) and kinases enables cells to sense and respond to environmental changes. The widely used chemical probe Pervanadate (PV) induces accumulation of high levels of pTyr in cells, an effect primarily attributed to its properties as a PTP inhibitor. This led to the assertion that PTPs are the master gatekeeper of intracellular pTyr homeostasis. Here, we use diverse approaches to reveal that PV disrupts cellular redox homeostasis and directly activates SRC family tyrosine kinases via oxidation of specific cysteine residues. Using mass spectrometry and biophysical approaches, we show that oxidation activates SRC by disrupting autoinhibition and altering phosphopeptide binding by its SH2 domain. We further establish that redox-sensitive cysteine residues are essential for SRC to promote cellular overgrowth. Our findings call for a re-evaluation of PV-based experiments and provide compelling evidence that oxidation is a crucial mechanism in controlling the oncogenic properties of SRC.

molecular biology↗

Altered auditory maturation in Fragile X syndrome and its involvement in audiogenic seizure susceptibility

BackgroundAuditory hypersensitivity is a prominent symptom in Fragile X syndrome (FXS), the most prevalent monogenic cause of autism and intellectual disability. FXS arises through the loss of the protein encoded by the FMR1 (Fragile X Messenger Ribonucleoprotein 1) gene, FMRP, required for normal neural circuit excitability. In the brainstem, FMRP is necessary for normal development of acoustic reactivity, and its loss has been implicated in audiogenic seizures (AGS) in Fmr1 knockout (KO) mice, modelling auditory hypersensitivity and seizures in FXS patients. PurposeThe present study investigated the correlation between auditory brainstem function and behavioral expression of AGS at the early (postnatal day P20, infancy) and late (P32, juvenile) stage of auditory development in Fmr1 KO mice compared with wildtype (WT) mice, and in both females and males. MethodsWe tested responsiveness to pure tones of select auditory pathway elements through auditory brainstem responses; and neural synchronization to amplitude envelopes of modulated acoustic stimuli through auditory steady-state responses. AGS behavior was categorized for severity during 5-minute exposure to loud sound. Expression of the immediate early gene cFos was quantified as a marker for neuronal activity in the inferior colliculus. ResultsDuring infancy, more severe AGS expression in Fmr1 KO mice compared with WT mice was accompanied by increased responsiveness to acoustic stimuli at the level of the superior olivary complex and inferior colliculus, and stronger neural synchronicity in subcortical auditory neurons. Fmr1 KO mice also had higher cFos positive cell counts in the inferior colliculus after exposure to loud sound. With age, both AGS susceptibility and exaggerated acoustic stimulus-evoked activity in the Fmr1 KO mice subsided. Intriguingly, Fmr1 KO mice displayed altered developmental profile in both the threshold and amplitude of auditory brainstem response. ConclusionOur findings support evidence that AGS activity relies upon hyperexcitability in the auditory system, including in the lower brainstem, possibly due to disturbed auditory maturation. Hyper-synchronization to modulated sounds in subcortical auditory neurons seemed to predict AGS severity. A better understanding of FXS-related circuit and behavioral symptoms of auditory processing across development provides the potential to identify therapeutic strategies to achieve auditory function recovery in FXS.

neuroscience↗

Mouse Forebrain Region-specific Molecular Characteristics and Cholinergic Neurons Subtyping: An Integrated Analysis Based on Spatial Multi-omics

The forebrain regions displays distinct yet under-characterized gene expression patterns. This study analyzed region-specific feature genes in forebrain regions and Isocortex sub-regions at both transcriptomic and proteomic levels. The key finding is the observation of low correlation but high functional similarity between mRNA and protein expression, which offers insights into the connection between gene expression forms in neuronal pathways and the neuronal activity state. Cholinergic neurons (CNs), play a vital role for the forebrains sensory and motor regulation. With Spatial-transcriptome and immunofluorescence joint analysis (STIF), which overcomes the limited resolution of the 10X Visium system, CNs- and CN-subtypes specific feature genes in the striatum and basal forebrain were identified, which providing crucial insights into the heterogeneity and functional diversity of these neuronal populations. The spatial distribution and expression pattern of the feature genes in this study were validated with either external datasets or rolling circle amplification-FISH, coincident results were revealed.

bioinformatics↗

Mapping AAV capsid sequences to functions through function-guided in silico evolution

Artificial intelligence (AI) offers significant potential to accelerate the functional engineering of adeno-associated virus (AAV) capsids in a time- and cost-efficient manner. However, existing approaches lack the ability to systematically map capsid sequences to multifunctional properties. To address this challenge, we developed ALICE, a knowledge-driven platform for in silico AAV capsid engineering that directly maps sequence to multiple functions. Our method incorporating a heuristic algorithm with contrastive learning principles, termed function-guided evolution (FE), to iteratively optimize high-performing capsid sequences generated by a naive language model toward desired functions. We elucidate FEs evolutionary mechanism, demonstrating its ability to navigate a function-guided landscape and generate capsids with tailored properties. After validating ALICEs ability to design murine-specific AAV capsids targeting Ly6a/Ly6c1 with limited training data, we developed ALICE-X by integrating a curriculum learning strategy. This upgrade facilitated exploration of sequence space beyond existing wet-lab datasets, enabling successful targeting of the human transferrin receptor 1 (hTfR1). The resulting engineered AAV variant, AAV.ALICE-H3, demonstrated improved viability, specific receptor targeting, and [~] 251-fold enhanced CNS tropism in human TFRC knock-in (hTFRC KI) mice compared to wildtype controls. This interpretable, knowledge-driven framework advances in silico AAV capsid design, offering broad applicability for translational gene therapy.

bioengineering↗

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Intracerebral hemorrhage (ICH) is a severe and widespread disease that results in high mortality and morbidity. Despite significant advances made in clinical and preclinical research, the prognosis of ICH remains poor due to an incomplete understanding of the complex pathological responses. To address this challenge, we generated single-cell resolution spatiotemporal transcriptomic maps of mouse brain 1, 3, 7, 14, and 28 days after ICH. Our analysis revealed the cellular constituents and their dynamic responses following ICH. We found changes in gene expression that are indicative of active phagocytosis and lipid processing in the lesion core and identified genes associated with brain repair at the lesion border. Persistent lipid accumulation culminated in the phenotypic transition of macrophages into foam cells. Furthermore, our results demonstrate that ICH could stimulate neural stem cells in the subventricular zone, thereby enhancing neurogenesis in this niche. This study provides a spatiotemporal molecular atlas of mouse ICH that advances the understanding of both local and global responses of brain cells to ICH and offers a valuable resource that can aid the development of novel therapies for this devastating condition.

neuroscience↗