Auditory Neurophysiology publications

Introduction: Learning-induced cortical reorganization is facilitated by neuromodulator release. However, the precise temporal relationship between neuromodulator release and neural activity required to induce plasticity is not well understood. In single synapses, eligibility traces regulate plasticity such that neuromodulator arrival must occur within seconds of activity. Cortical plasticity can also be induced by pairing neuromodulator release with neural activity, but it is unknown whether plasticity in populations of neurons is regulated by the same temporal constraints. Methods: To determine whether the synaptic eligibility trace regulates cortical plasticity, we used vagus nerve stimulation (VNS) to drive neuromodulator release 3 s before, 1 s before, concurrent with, or 3 s after tone-evoked activity in auditory cortex. After 20 days of pairing, we used in vivo electrophysiology to quantify the proportion of auditory cortex responding to the paired tone frequency. Results: We found that VNS 1 s before or concurrent with tone onset significantly expanded the representation of the paired tone frequency (-1s, p = 0.04; 0s, p = 0.02), whereas 3 s before or after did not (-3s, p = 0.87; +3s, p = 0.53). Confirming the role of neuromodulators in this eligibility trace, we found that depletion of norepinephrine prevented VNS-tone pairing-induced plasticity (0s + DSP4, p = 0.23). Discussion: Our study demonstrates that cortical plasticity is regulated by time constraints similar to the synaptic eligibility trace and highlights the importance of considering the timing of neuromodulator release when employing methods to enhance plasticity.

In adults with acquired hearing loss, cortical reorganization and cross‐modal plasticity critically influence the timing and outcomes of cochlear implantation. This study examined the effects of 2 weeks of bilateral auditory deprivation—induced by intense broadband noise—on the structure and gene expression in the primary auditory (A1) and visual (V1) cortices of adult rats. The results revealed that the total neuronal counts in both the A1 and V1 remained unchanged compared to controls. Morphological analysis showed no significant change in mature dendritic spine density in either region, but immature spine density was significantly reduced in the V1 cortex. Ultrastructural examination demonstrated notable synaptic alterations in the A1 cortex, including significant reductions in postsynaptic density (PSD) length, thickness, area, and synaptic vesicle number—changes that were not observed in the V1 cortex. Transcriptomic profiling indicated a region‐specific response, with 197 differentially expressed genes (DEGs) in the A1 cortex, compared to a broader alteration of 545 DEGs in the V1 cortex, which were significantly involved in neuronal signaling and synaptic transmission. These findings demonstrate that auditory deprivation induces distinct molecular and synaptic remodeling in the A1 and V1 cortices, identifying neuronal plasticity and synaptic regulation as central mechanisms for cross‐modal reorganization in the adult brain.

Large language models (LLMs) capture long-range contextual structure in natural language and have recently been shown to align with the human brain’s contextualized linguistic encoding. This makes them a promising computational probe for studying how context-dependent linguistic information is represented during natural speech perception. Speech perception often occurs in multi-talker environments, where attention must dynamically select among competing streams, yet how contextual information from attended and unattended speech is neurally encoded remains underexplored. Here, we investigate how auditory attention modulates neural tracking of context-dependent linguistic representations using electrocorticography (ECoG) and stereoelectroencephalography (sEEG) recordings from three epilepsy patients engaged in a two-conversation “cocktail party” paradigm. To model neural responses to attended and unattended speech streams, we used contextual word embeddings generated by large language models. We find that LLM-derived features reliably predict brain activity for the attended stream and that contextual information from the unattended stream also contributes to neural prediction. Importantly, these contributions extend beyond low-level acoustic features and shallow syntactic information, and depend on the surrounding linguistic context. Moreover, neural tracking of the unattended stream reflects shorter-range contextual integration than that of the attended stream. Together, these findings indicate that neural responses to speech reflect context-dependent linguistic representations from multiple concurrent speech streams, with attention modulating the depth and timescale of contextual integration. Our results highlight the utility of LLMs for probing higher-level linguistic representations in complex, naturalistic listening environments.

The hippocampus is classically linked to memory, yet increasing evidence points to a broader role in perceptual inference and deviance detection. Predictive coding theories propose that perception minimizes mismatches between expected and actual sensory input, expressed in neural signatures such as mismatch negativity (MMN) and P300. Although MMN arises mainly from sensory and prefrontal cortices, the hippocampus is anatomically interconnected with both and may also contribute to prediction error processing. We recorded single- and multi-unit activity and local field potentials (LFPs) from DG and CA1 in urethane-anesthetized rats during an auditory oddball paradigm and a no-repetition control sequence to dissociate prediction error from repetition suppression. Approximately 20% of hippocampal neurons were sound responsive, and a subset showed deviant selectivity. Spiking activity predominantly reflected prediction errors, while LFPs revealed complementary contributions from repetition suppression and prediction error. Early LFP components were enhanced for randomly presented deviants, whereas later components within the P300 latency range were stronger for predictable deviants, indicating temporally distinct phases of error signaling and top-down modulation. These findings identify the hippocampus as an active contributor to auditory deviance detection and support a hierarchical model in which hippocampal circuits participate in predictive sensory processing beyond memory.

Auditory 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, modeling auditory hypersensitivity and seizures in FXS patients. The 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) stages of auditory development in Fmr1 KO mice compared with wildtype (WT) mice, and in both females and males. We 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‐min exposure to loud sound. Expression of the immediate early gene cFos was quantified as a marker for neuronal activity in the inferior colliculus. During 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 an altered developmental profile in both the threshold and amplitude of auditory brainstem response. Our 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. The developmental trajectory of the auditory hyperresponsiveness and hypersynchrony suggests a transient processing alteration underlying heightened AGS susceptibility in Fmr1 KO mice. 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.

Purpose Although human temporal bones suggest that cochlear synapse numbers decline with age and noise exposure, no validated diagnostic method exists. In animal models, cochlear synaptopathy is associated with reduced auditory brainstem response (ABR) wave 1 amplitude and envelope following response (EFR) magnitude for a sinusoidally amplitude modulated (SAM) tone. However, measuring SAM EFR at the optimal modulation frequency (1000 Hz) is difficult in humans. A rectangular amplitude modulated (RAM) tone may be more sensitive to synaptopathy, but this has not been validated in animals. In addition, because synaptopathy likely co-occurs with outer hair cell dysfunction (OHC), a diagnostic assay needs to be robust to abnormal auditory thresholds. The objective of this study was to evaluate the relative ability of ABR and EFR measures to predict synapse numbers in mice with varying degrees of synaptopathy and OHC dysfunction. Methods Distortion product otoacoustic emissions (DPOAEs), ABR, SAM EFR, and RAM EFR were recorded from 57 mice with a range of auditory thresholds and degrees of synaptopathy. Cross-validation was used to compare the relative ability of linear regression models incorporating different measures to predict synapse numbers. Predictions were confirmed histologically. Results RAM EFR modulated at 1000 Hz was the single best predictor of synapse numbers for broad synapse loss across frequency, while combining RAM EFR with ABR further improved predictions. In contrast, ABR best predicted focal synaptopathy. Incorporating DPOAEs improved predictions for EFR, but not ABR. Conclusion RAM EFR, ABR, and DPOAEs should be used in the future when predicting synapse numbers.

Recent studies suggest some hippocampal (HC) neurons respond to passively presented sounds in naive subjects, but the specificity and prevalence of these responses remain unclear. We used Neuropixels probes to record unit activity across layers in mid-ventral HC and auditory cortex (ACtx) of awake, untrained mice (male and female) while presenting diverse sounds at typical environmental levels (65–70 dB SPL). A subset of HC neurons exhibited reliable, short latency responses to passive sounds, including tones and broadband noise. HC units showed evidence of tuning for tone frequency but not spectrotemporal features in continuous dynamic moving ripples. Across sound types, HC responses overwhelmingly occurred at stimulus onset; they quickly adapted to continuous sounds and did not respond at sound offset. Among all sounds tested, broadband noise was most effective at driving HC activity. Spectral manipulations indicated response prevalence scaled with increasing spectral bandwidth and density. Similar responses were also observed for visual flash and contrast-modulated noise movies, although these were less common than for broadband noise. Sound-evoked face movements, quantified by total face motion energy (FME), correlated with population-level HC activity. However, many individual units responded regardless of FME strength, suggesting both auditory and motor-correlated inputs. Together, our results show that abrupt sound onsets are sufficient to activate many HC neurons in the absence of learning or behavioral engagement. This supports a role for HC in detecting salient environmental changes and supports the idea that auditory inputs contribute directly to HC function.

The cochlear implant is a widely available hearing restoration technology that can provide speech understanding in quiet environments. This technology struggles however, in noisy settings or situations involving multiple speakers. The primary cause of these performance limitations is a poor neural interface, in which the bony wall of the cochlea separates the electrode surface from the auditory nerve fibers, thus causing unwanted current spread and non-specific frequency activation. This study utilizes an alternative auditory prosthetic technology (auditory nerve implant, ANI) that enables direct auditory nerve stimulation, which provides a potentially superior neural interface and enables more precise targeting of auditory nerve fibers than traditional cochlear implants. As auditory nerve implants progress towards clinical translation, new implant designs and stimulation strategies will be created. Animal models to efficiently test and iterate through these new designs will be useful for the continued development of ANI technology. We present a viable surgical approach in the non-human primate (rhesus macaque) along with electrophysiological results that demonstrate robust activation of the auditory system at low current levels via intraneural stimulation. Our findings indicate that the rhesus macaque, which possesses an inner ear anatomy more similar to the human compared to other animal models used in the hearing field (e.g., rodents, felines and ferrets), has strong potential as a useful preclinical testbed involving an upright head model for future ANI prototypes and stimulation strategy development.

Stories, Chirps, And Noisy Sentences (MEG-SCANS) is a dataset that provides raw magnetoencephalography (MEG) recordings from 24 German-speaking subjects. Each subject listened to approximately one hour of stimuli, including two audiobooks, sentences from the Oldenburger Matrix Sentence Test (OLSA) for Speech Reception Threshold (SRT) assessment, and short up-chirps used to assess MEG signal quality. The dataset includes MEG data, structural MRI (Magnetic Resonance Imaging) scans of the head, corresponding audio material (audiobooks, OLSA envelopes, and chirp stimuli), and behavioral audiogram and SRT results from hearing screenings. Organized according to the Brain Imaging Data Structure (BIDS), this resource offers a robust benchmark for large-scale encoding/decoding analyses of temporally-resolved brain responses to speech. Comprehensive Matlab and Python code are included to replicate key data validations, ensuring transparency and reproducibility.

The insula is critical for integrating sensory information from the body with that arising from the environment. Although previous studies suggested that posterior insula is sensitive to sounds, these studies usually involved behaviorally relevant stimuli. Further, auditory response properties of the human insula have not previously been studied on the single neuron level. Here, we provide the first report of a population of human single neuron data from both anterior and posterior insula and provide comparative data from the primary auditory cortex, recorded intracranially from human participants during passive listening. In each condition, more than 340 single neurons were recorded in 12 participants of either sex. Almost a third of neurons in posterior insula and a smaller subset in anterior insula responded to simple tones and clicks. Responsive neurons were distributed throughout posterior and anterior insula and showed preferred frequency tuning. Onset latencies in insula were short, but response durations were significantly shorter than primary auditory cortex. Overall, these data show that insula neurons respond to auditory stimuli even in nonbehaviorally relevant contexts and change our understanding of this brain region, suggesting that processing basic auditory stimuli is an important integrative function of insular cortex.

Sensorineural hearing loss (SNHL) caused by human cytomegalovirus (HCMV) infection involves alterations in both the central auditory pathways and cochlear structures. Immediate early (IE) proteins are critical for HCMV pathogenicity and have been associated with neurodevelopmental disorders; however, their contribution to HCMV-associated SNHL remains unclear. Here, we generated transgenic mouse models expressing HCMV IE1 and IE2 protein to investigate their effects on auditory function and cochlear pathology. Auditory brainstem response (ABR) measurements revealed that expression of IE2, but not IE1, led to significantly elevated ABR thresholds and impaired auditory processing. IE2-transgenic mice exhibited synaptic loss, hair cell degeneration, and neuronal atrophy in auditory regions. scRNA-seq analysis indicated broad activation of inflammatory pathways and cytokines within the cochlea, along with disruptions in mitochondrial and metabolic pathways, suggesting that IE2 may contribute to hearing loss through mitochondrial impairment and inflammation. Transmission electron microscopy of cochlear tissues showed severe morphological abnormalities and a marked reduction in mitochondrial number in spiral ganglion neurons (SGNs). Further mechanistic investigation demonstrated that IE2 interacts with TSC2, leading to hyperactivation of mTOR signaling, metabolic dysregulation, and mitochondrial dysfunction. Importantly, administration of mTOR inhibitors substantially alleviated IE2-induced auditory deficits, hair cell degeneration, and neuronal atrophy. These findings identify IE2 through TSC2-mTOR-mediated mitochondrial dysfunction, metabolic reprogramming, and neuroinflammation leading to SNHL. Our study reveals a previously unrecognized mechanism linking IE2 protein expression to auditory neurodegeneration and suggests mTOR modulation as a potential therapeutic strategy for congenital HCMV infection and associated hearing loss.

Noise-induced hearing loss can lead to degeneration of spiral ganglion neurons (SGN), resulting in impairment of auditory signalling. However, the specific mechanism is unclear. In our study, we investigated the function of mitochondrial activity following noise exposure. Findings revealed a reduction in ATP synthesis and alterations in the levels of mitochondrial electron transport chain complexes II, Ⅲ, IV and complex I subunit ND3 reduction by the seventh day post-noise exposure. These findings indicate that SGN mitochondrial dysfunction can impair SGN function. This is further demonstrated by the reduced expression of the mitochondrial marker protein Tom20 and apoptosis-inducing factor (AIF) showed inner membrane but not outer membrane resulted in changes in mitochondrial ETC complexes. And the findings of calpain 2 but not calpain 1 high expression was accompanied in AIF reduction, suggesting AIF has not yet caused SGN deaths. Calpain 2 regulated decreased expression of AIF may relieve the low function of mitochondrion in SGN after noise.

Tinnitus, the perception of a phantom sound, often occurs as a clinical sequela of auditory traumas. However, the underlying mechanisms of tinnitus are largely unknown. In our previous studies, we found more gamma-aminobutyric acid A receptor alpha 1 subunit (GABAAR-α1)-positive cells in the dorsal cochlear nucleus (DCN) after noise exposure, however, we were not able to identify the specific types of DCN cells that up-regulated GABAAR-α1 after the insult. In the current study, we used Nissl staining, Purkinje cell protein 4 (PCP4) and glutamic acid decarboxylase 67 (GAD67) immunolabeling to identify GABAAR-α1-positive cells in the DCN. Each type of GABAAR-α1-positive cells was quantified and statistically analyzed using immunostaining and Nissl staining according to their morphology, size and location in the DCN. GABAAR-α1-positive cartwheel cells, Golgi cells, as well as ML-stellate and vertical cells were confirmed by dual immunolabeling. In the DCN, the most common GABAAR-α1-positive cells were Golgi cells followed by vertical cells and cartwheel cells while very few other cells were GABAAR-α1-positive in all conditions. We found significantly more GABAAR-α1-positive Golgi cells in the DCN of noise-exposed rats without behavioral evidence of tinnitus compared to normal controls and noise-exposed rats with behavioral evidence of tinnitus. This heightened "context-dependent" inhibition may help to maintain a balanced neuronal network, preventing the potential for tinnitus-related hyperactivity in the auditory pathways.

Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane (TM)-attachment crowns (ACs), anchoring the tallest stereocilia to the TM. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identifies TMEM145, a transmembrane protein with a Golgi dynamics domain, as a crucial OHC stereocilia component. TMEM145 is expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibit profound hearing impairment at 3 weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy reveal the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacts with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 is undetectable in Stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

Species recognition is essential for reproductive isolation and plays a central role in the evolution of mating signals. In acoustically communicating species, temporal features of calls are critical for distinguishing conspecific from heterospecific signals. Anurans rely heavily on the precise timing of pulse trains for mate recognition. Females of Hyla chrysoscelis use the species-specific temporal structure of male advertisement (Adv) calls-specifically pulse rate (PR)-to select mates. For stimuli with the Adv call PR (40-60 pulses/s), females require at least ~ 6-7 pulses to approach a sound source, implicating interval-counting neurons (ICNs) in call recognition. To test this model and further investigate the neural basis of this temporal selectivity, we used behavioral and neurophysiological approaches. We lengthened interpulse intervals (IPIs) in pulse trains either at a single midpoint or in an alternating fashion while holding pulse number and, thus, stimulus energy constant. In phonotaxis assays, females showed sharply reduced responses when even one IPI was lengthened twofold or more, revealing high sensitivity to temporal irregularity. Single-unit in vivo extracellular recordings from the auditory midbrain revealed that ICNs exhibited a progressive decline in activity with increasing IPI length, closely mirroring behavioral trends. In contrast, long-interval neurons (LINs) responded more strongly to temporally irregular stimuli. These results support the hypothesis that ICNs mediate behavioral selectivity for conspecific Adv call temporal patterns, whereas LINs may contribute to processing other call types. Our study directly links a defined neuronal population to natural behavior, underscoring how midbrain temporal computations underlie species-specific recognition in Hyla chrysoscelis.

Objective. Infrared neural stimulation (INS) has emerged as a potent neuromodulation technology, offering safe and focal stimulation with superior spatial recruitment profiles compared to conventional electrical methods. However, the neural dynamics induced by INS stimulation remain poorly understood. Elucidating these dynamics will help develop new INS stimulation paradigms and advance its clinical application. Approach. In this study, we assessed the local network dynamics of INS entrainment in the auditory thalamocortical circuit using the chronically implanted rat model. Our approach focused on measuring INS energy-based local field potential (LFP) recruitment induced by focal thalamocortical stimulation. We further characterized linear and nonlinear oscillatory LFP activity in response to single-pulse and periodic INS and performed spectral decomposition to uncover specific LFP band entrainment to INS. Finally, we examined spike-field transformations across the thalamocortical synapse using spike-LFP coherence coupling measures. Main results. We found that INS significantly increases LFP amplitude as a log-linear function of INS energy per pulse, primarily entraining to LFP β and γ bands with synchrony extending to 200 Hz in some cases. A subset of neurons demonstrated nonlinear, chaotic oscillations linked to information transfer across cortical circuits. Finally, we utilized spike-field coherences to correlate spike coupling to LFP frequency band activity and suggest an energy-dependent model of network activation resulting from INS stimulation. Significance. We show that INS reliably drives robust network activity and can potently modulate cortical field potentials across a wide range of frequencies in a stimulus parameter-dependent manner. Based on these results, we propose design principles for developing full coverage, all-optical thalamocortical auditory neuroprostheses.

Noise-induced hearing loss (NIHL) is a primary contributor to tinnitus, involving mechanisms such as inflammatory damage, central sensitization, and auditory cortex remodeling. However, not all cases of tinnitus are accompanied by NIHL, and the precise relationship between the two remains incompletely understood. Phosphorylation/dephosphorylation, as a core mechanism for fine cellular regulation, influences neuronal excitability, immune responses, and disease development by modulating protein activity, signal transduction, and gene expression. We hypothesized that aberrant phosphorylation levels may alter auditory cortex neuron function, leading to pathological changes at the protein level. Leveraging auditory cortex tissue from a noise-induced tinnitus model, we systematically investigated the pathogenesis of tinnitus and its distinction from NIHL through integrated proteomic and phosphoproteomic analyses. Compared to animals with NIHL alone, the tinnitus model exhibited enhanced neuronal excitability, synaptic dysfunction, hyperactive energy metabolism, and weakened neuroprotection, with disordered membrane receptor function playing a critical role. Multi-omics analysis further revealed that tinnitus development primarily depends on phosphorylation-mediated post-translational modifications reshaping cellular function, rather than changes in protein abundance caused by alterations in gene transcription levels. Collectively, this study elucidates the physiological and cellular structural alterations in noise-induced tinnitus from the dimensions of protein expression and phosphorylation modification. It confirms that tinnitus leads to neural dysfunction through abnormal membrane receptor activity, and the characteristic proteins and phosphorylation sites identified offer novel therapeutic targets for modulating central hyperexcitability in tinnitus.

The thalamocortical pathways exhibit neuroplasticity not only during the critical period but also in adulthood. In this study, we investigated how cholecystokinin (CCK) modulates age-dependent thalamocortical plasticity. Our findings demonstrated that CCK is expressed in thalamocortical neurons and that high-frequency stimulation (HFS) of the thalamocortical pathway triggers the release of CCK in auditory cortex (ACx), as detected by a CCK sensor. HFS of the medial geniculate body (MGB) induced thalamocortical long-term potentiation (LTP) in wild-type young adult mice. However, knockdown of CCK expression in MGB neurons or blockade of the CCK-B receptor (CCKBR) in the ACx abolished HFS-induced LTP. Interestingly, this LTP could not be elicited in juvenile (3-week-old) or aged mice (over 18-month-old) due to distinct mechanisms: the absence of CCKBR in juveniles and the inability to release CCK in aged mice. Notably, exogenous administration of CCK into the ACx rescued LTP in aged mice and significantly improved frequency discrimination. These findings highlight the potential of CCK as a therapeutic intervention for ameliorating neuroplasticity deficits associated with thalamocortical connectivity.

During wake, sound‐evoked and spontaneous neural activity of the auditory cortex evolves in distinct subspaces, whereas anesthesia disrupts sound responses and merges these spaces. To evaluate if similar modifications of sound representation geometry explain sensory disconnection during sleep, large neural populations of the mouse auditory cortex are followed across slow‐wave sleep and wakefulness. It is observed that sleep dampens sound responses but preserves the geometry of sound representations such that they remain separate from spontaneous activity. Moreover, response dampening is strongly coordinated across neurons and varied throughout sleep, spanning from fully preserved response patterns to population response failures on a fraction of sound presentations. These failures rarely occurred in wakefulness and are more common during high spindle‐band activity. Therefore, in sleep, the auditory system preserves sound feature selectivity up to the cortex for detailed acoustic surveillance but concurrently implements an intermittent gating mechanism leading to local sensory disconnections.

Background CLN3 disease, also known as juvenile Batten disease, is a recessively inherited neurodevelopmental disorder caused by mutations in the CLN3 gene. It represents the most common form of Neuronal Ceroid Lipofuscinoses (NCLs), a group of lysosomal storage disorders that impair brain function. Clinical features include progressive vision loss, language impairment, and cognitive decline. The early onset of visual deficits complicates the neurological assessment of cognitive dysfunction, while the rarity of CLN3 cases limits the study of sex-specific disease trajectories in humans. Therefore, there is a critical need for objective, translational biomarkers to monitor disease progression and support therapeutic development in preclinical animal models. Methods Building on our recent studies in individuals with CLN3 disease, we developed a parallel experimental paradigm using high-density electroencephalography (EEG) in Cln3 knockout ( Cln3-/-) mice to longitudinally assess auditory neurophysiological changes. We applied a duration-based mismatch negativity (MMN) paradigm, similar to that used in our human studies, to evaluate automatic detection of auditory pattern changes in male and female mice between 3 and 9 months of age. Results Wild-type (WT) mice of both sexes showed robust and stable duration MMN responses across this age range. In contrast, Cln3-/- mice showed marked sex- and age-dependent deficits: female mutants displayed persistent MMN deficits, whereas male mutants exhibited early MMN abnormalities that unexpectedly improved with age. Auditory brainstem responses confirmed intact peripheral hearing in Cln3-/- mice, indicating a central origin for the observed abnormalities. Further analyses revealed that MMN impairments were driven by age- and sex-specific alterations in auditory evoked potentials to both standard and deviant stimuli. Conclusions These findings demonstrate sex- and age-dependent disruptions in central auditory processing in Cln3-/- mice and support auditory duration MMN as a sensitive, translational biomarker of brain dysfunction in CLN3 disease. This approach offers a functional, cross-species measure for tracking disease progression and evaluating therapeutic interventions in Batten disease.