Biology subjects

Sridhar, S.

Publications and source records attributed to Sridhar, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Repetitive Levodopa Treatment Drives Cell Type-Specific Striatal Adaptations Associated With Progressive Dyskinesia in Parkinsonian Mice

The use of levodopa to manage Parkinsons disease (PD) symptoms leads to levodopa-induced dyskinesia (LID) and other motor fluctuations, which worsen with disease progression and repeated treatment. Aberrant activity of striatal D1- and D2-expressing medium spiny neurons (D1-/D2-MSNs) underlies LID, but the mechanisms driving its progression remain unclear. Using the 6-OHDA mouse model of PD/LID, we combined in vivo and ex vivo recordings to isolate the effect of repeated treatment in LID worsening and other motor fluctuation-related phenotypes. We found that LID worsening is linked to potentiation of levodopa-evoked responses in both D1-/D2-MSNs, independent of changes in dopamine release or MSN intrinsic excitability. Instead, strengthening of glutamatergic synapses onto D1-MSNs emerged as a key driver. Moreover, we found changes in D2-MSN activity that specifically influenced LID duration, potentially contributing to motor fluctuations, which paralleled a reduction in D2R sensitivity. These findings reveal striatal adaptations contributing to worsening of levodopa-related complications.

neuroscience↗

bioRxiv2025

Closed-loop sonothermogenetic control of CAR T cells for metronomic brain cancer therapy

Achieving durable CAR T cell responses against primary brain tumors and metastases requires strategies that enable intracranial control of therapy to overcome the barriers of solid tumor treatment without compromising safety. Here, we show that closed-loop sonothermogenetics enables remote regulation of CAR T cell therapeutic activity through the intact skull. Using MR-guided focused ultrasound with closed-loop temperature feedback, we modulate CAR T cells engineered with a genetically encoded thermal bioswitch to achieve metronomic activation in the brain without lasting adverse effects on healthy brain tissue. In murine models of brain cancer, metronomic production of NKG2D T cell engagers by intratumoral CAR T cells overcomes antigen heterogeneity in breast cancer brain metastasis and myeloid-derived immunosuppression in glioblastoma to drive antitumor responses. Our findings support the use of closed-loop sonothermogenetics for spatial and temporal control of CAR T cell therapies targeting solid brain tumors.

bioengineering↗

bioRxiv2025

Spatial Adaptation of Primate Retinal Ganglion Cells between Artificial and Natural Stimuli

The retina encodes a broad range of stimuli, adapting its computations to features like brightness, contrast, or motion. However, it is unclear to what extent it also adapts to spatial frequency content - as theories of efficient coding would predict - for instance, when switching between natural scenes and white noise. To address this, we analyzed neural activity of marmoset retinal ganglion cells (RGCs) in response to white noise and naturalistic movie stimuli. We trained linear-nonlinear models on both stimuli, evaluated their performance and compared their receptive fields (RFs) across the stimulus domains. We found that the models with spatial filters trained on either one of the stimulus ensembles were not able to predict the neural activity on the other as accurately as the models trained on the target stimulus. This suggests that spatial processing adapts to stimulus statistics. Different RGC types exhibited distinct changes: the midget OFF cells RFs became enlarged under natural movie statistics, resulting in a lower cutoff frequency. Parasol cells did not change their RF size significantly. Large OFF cells RFs decreased in size. All cell types exhibited stronger surrounds under natural movies, resembling the whitening filters predicted by efficient coding. However, quantifying the effect of the filter adaptation on the stimulus power spectrum showed a significant contribution towards whitening only in ON parasol cells. The whitening effect emerged regardless of the training stimulus. These results suggest that while RGCs adapt to the spatial frequency content of the input, efficient coding can only partially account for this adaptation. Significance statementNatural scenes differ from artificial stimuli like white noise, in spatial frequency structure. How the retina adapts to these differences remains unclear. To explore this, we studied responses of four primate retinal ganglion cell types to artificial and natural stimuli. Our results show that some cell types, like midget cells, enlarge their receptive fields and surrounds under natural stimuli, while others, like parasol cells, only enhance surrounds. These changes align qualitatively with the efficient coding theory, which posits redundancy reduction. However, in three cell types, the enhanced surrounds did not significantly whiten responses to natural stimuli, contrary to efficient coding predictions. These findings challenge how fully efficient coding explains retinal adaptation, suggesting that other principles underlie the processing of visual inputs.

systems biology↗

bioRxiv2025

Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers

Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers frequently acquire AMR organisms, and thus may provide a window into AMR dynamics in otherwise poorly monitored regions and environments. To assess the utility of travelers as global AMR sentinels, we collected pre- and post-travel stool samples from 608 travelers, which were screened for the presence of extended-spectrum beta-lactamase producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales. A total of 307 distinct AMR organisms were sequenced in order to determine genotypic patterns and their association with travel region and behavior. Travel-associated AMR organisms were overwhelmingly E. coli, which exhibited considerable phylogenetic diversity regardless of travel region. However, the prevalence of resistance genes varied by region, with blaCTX-M-55 and blaCTX-M-27 significantly more common in travelers returning from South America and South-Eastern Asia, respectively. Hybrid assembly and plasmid reconstruction revealed the genomic neighborhood of blaCTX-M-55 frequently matched a motif previously linked to animal populations. Contact with animals was also associated with virulence factors in acquired AMR organisms, including carriage of the ColV plasmid, a driver of avian pathogenic E. coli. We identified novel variants of the mcr-1 gene in strains acquired from Western Africa, highlighting the potential for traveler surveillance to detect emerging clinical threats. Ongoing efforts to track travel-acquired organisms could complement existing global AMR surveillance frameworks. ImportanceWe collected pre- and post-travel stool samples from 608 U.S. international travelers, which were screened for the presence of three clinically relevant antimicrobial-resistant organisms, with the goal of understanding the utility of travelers as sentinels for emerging AMR and identifying regional resistance patterns. We sequenced 307 organisms and uncovered significant diversity and geographic heterogeneity in AMR organisms. We found significant differences in certain resistance gene alleles of travelers returning from South America and South-Eastern Asia, traveler contact with animals associated with virulence factors, including a plasmid that is a known driver of avian pathogenic E. coli, and novel variants of the colistin resistance mcr-1 gene in strains acquired from Western Africa. This work emphasizes the value of monitoring international travelers as a proxy for understanding AMR patterns globally and could be an important addition to existing global AMR surveillance frameworks.

genomics↗

bioRxiv2025

Development of an RT-RPA assay for La Crosse virus detection provides insights into age-dependent neuroinvasion in mice

BackgroundLa Crosse virus (LACV) is a mosquito-borne arbovirus responsible for pediatric encephalitis in North America, predominantly affecting children under 16 years. Early and accurate diagnosis is critical to reducing morbidity in this vulnerable population. However, existing molecular and serological methods are limited in sensitivity, specificity, and accessibility. MethodsTo address these limitations, we developed a reverse transcription recombinase polymerase amplification (RT-RPA) assay for LACV detection. Primers targeting the divergent M segment of the LACV genome were designed and screened for optimal performance. The assays analytical sensitivity was evaluated through serial dilutions of LACV RNA prior to reverse transcription, while specificity was assessed using reverse transcribed RNA from related or geographically relevant arboviruses. We further adapted the RT-RPA test into a lateral flow assay (LFA) format for potential point-of-care use. Additionally, we employed a murine model to explore the age-dependent dynamics of LACV neuroinvasion and clearance, with the virus detected using RT-RPA and reverse transcription quantitative polymerase change reaction (RT-qPCR). ResultsPrimer screening identified an optimal primer pair that amplified LACV cDNA within 20 minutes at 39{degrees}C, with a limit of detection (LOD) of 100 copies. The assay demonstrated high specificity, with no amplification of related or other geographically relevant arboviruses. Integration of the RT-RPA test into an LFA format preserved the LOD and specificity, enabling visual detection via test strips. In the murine model, weanling mice exhibited LACV neuroinvasion as early as 4 days post-infection (dpi), with sustained detection between 5-7 dpi. In adult mice, neuroinvasion was first detected at 5 dpi, plateauing between 6-10 dpi, and cleared entirely by 20 dpi in surviving animals. ConclusionsThis study establishes the RT-RPA assay as an efficient, specific, and sensitive diagnostic platform for LACV, with potential for adaptation into field-deployable LFA tests. Moreover, our findings provide valuable insights into the age-dependent dynamics of LACV neuroinvasion and clearance, informing future diagnostic and therapeutic strategies.

microbiology↗

bioRxiv2024

ecPath detects ecDNA in tumors from histopathology images

Circular extrachromosomal DNA (ecDNA) can drive tumor initiation, progression and resistance in some of the most aggressive cancers and is emerging as a promising anti-cancer target. However, detection currently requires costly whole-genome sequencing (WGS) or labor-intensive cytogenetic or FISH imaging, limiting its application in routine clinical diagnosis. To overcome this, we developed ecPath (ecDNA from histopathology), a computational method for predicting ecDNA status from routinely available hematoxylin and eosin (H&E) images. ecPath implements a deep-learning method we call transcriptomics-guided learning, which utilizes both transcriptomics and H&E images during the training phase to enable successful ecDNA prediction from H&E images alone, a task not achievable with models trained on H&E images only. It is trained on more than 6,000 tumor whole-slide images from the TCGA cohort with the best performance in predicting ecDNA status in brain and stomach tumors (average AUC=0.78). ecPath revealed that ecDNA-positive tumors are enriched with pleomorphic, larger and high-density nuclei. Testing in an independent cohort, ecPath predicted ecDNA status of 985 pediatric brain tumor patients with an AUC of 0.72. Finally, we applied ecPath to identify ecDNA-positive tumors in the TCGA cohort for which no WGS data were available. Like WGS-based ecDNA-positive labels, the predicted ecDNA-positive status also identify poor prognoses for low grade glioma patients. These results demonstrate that ecPath enables the detection of ecDNA from routinely available H&E imaging alone and help nominate aggressive tumors with ecDNA to study and target it.

pathology↗

bioRxiv2024

Striatal lateral inhibition regulates action selection in a mouse model of levodopa-induced dyskinesia

Striatal medium spiny neurons (MSNs) integrate convergent cortical, thalamic, and dopaminergic inputs to shape motor output. In addition, MSNs form local inhibitory synaptic connections with one another. The function of this striatal lateral inhibition is unknown, but one possibility is in selecting an intended action while suppressing alternatives. The execution of selected movements is disrupted in several movement disorders, including levodopa-induced dyskinesia (LID), a complication of Parkinsons disease (PD) therapy characterized by involuntary movements. Here, we identify chronic changes in the strength of striatal lateral inhibitory synapses in a mouse model of PD/LID. These synapses are also modulated by acute dopamine signaling. Chemogenetic suppression of lateral inhibition originating from dopamine D2 receptor-expressing MSNs lowers the threshold to develop involuntary movements in vivo. By comparing striatal lateral inhibition in health and PD/LID, our findings support a role for this microcircuit in movement selection and suggest its disruption may increase vulnerability to dyskinesia.

neuroscience↗

bioRxiv2024

Tau P301S Transgenic Mice Develop Gait and Eye Movement Impairments That Mimic Progressive Supranuclear Palsy

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder with an estimated prevalence of 5-7 people in 100,000. Clinically characterized by impairments in gait, balance, and eye movements, as well as aggregated Tau pathology, PSP leads to death in approximately 5-8 years. No disease-modifying treatments are currently available. The contribution of Tau pathology to the symptoms of patients with PSP is poorly understood, in part due to lack of a rodent model that recapitulates characteristic aspects of PSP. Here, we assessed the hTau.P301S mouse for key clinical features of PSP, finding progressive impairments in balance and gait coordination. Additionally, we found impairments in fast vertical eye movements, one of the most distinctive features of PSP. Across animals, we found that Tau pathology in motor control regions correlated with motor deficits. These findings highlight the utility of the hP301S mouse in modeling key aspects of PSP.

neuroscience↗

bioRxiv2024

Aerosol delivery of immunotherapy and Hesperetin-loaded nanoparticles increases survival in a murine lung cancer model

PurposeStudies have shown that flavonoids like Hesperetin, an ACE2 receptor agonist with antioxidant and pro-apoptotic activity, can induce apoptosis in cancer cells. ACE2 receptors are abundant in lung cancer cells. Here, we explored the application of Hesperetin bound to PLGA-coated nanoparticles (Hesperetin-nanoparticles, HNPs), and anti-CD40 antibody as an aerosol treatment for lung tumor-bearing mice. MethodsIn-vitro and in-vivo studies were performed in human A549 (ATCC) and murine LLC1 (ATCC) lung cancer cell lines. Hesperetin Nanoparticles (HNP) of about 60nm diameter were engineered using a nano-formulation microfluidic technique. A syngeneic orthotopic murine model of lung adenoma was generated in wild (+/+) C57/BL6 background mice with luciferase-positive cell line LLC1 cells. Lung tumor-bearing mice were treated via aerosol inhalation with HNP, anti-CD40 antibody, or both. Survival was used to analyze the efficacy of aerosol treatment. Cohorts were also analyzed for body condition score, weight, and liver and kidney function. ResultsAnalysis of an orthotopic murine lung cancer model demonstrates a differential uptake of the HNP and anti-CD40 by cancer cells relative to normal cells. A higher survival rate, relative to untreated controls, was observed when aerosol treatment with HNP was added to treatment via anti-CD40 (p<0.001), as compared to CD40 alone (p<0.01). Moreover, 2 out of 9 tumor-bearing mice survived long term, and their tumors diminished. These 2 mice were shown to be refractory to subsequent development of subcutaneous tumors, indicating systemic resilience to tumor formation. ConclusionWe successfully established increased therapeutic efficacy of anti-CD40 and HNP in an orthotopic murine lung cancer model using inhalation-based administration. Our findings open the possibility of improved lung cancer treatment using flavonoids and immuno-adjuvants.

bioengineering↗

bioRxiv2024

Beta-frequency sensory stimulation enhances gait rhythmicity through strengthened coupling between striatal networks and stepping movement

Stepping movement is delta (1-4 Hz) rhythmic and depends on sensory inputs. In addition to delta rhythms, beta (10-30 Hz) frequency dynamics are also prominent in the motor circuits and are coupled to neuronal delta rhythms both at the network and the cellular levels. Since beta rhythms are broadly supported by cortical and subcortical sensorimotor circuits, we explore how beta-frequency sensory stimulation influences delta-rhythmic stepping movement, and dorsal striatal circuit regulation of stepping. We delivered audiovisual stimulation at 10 Hz or 145 Hz to mice voluntarily locomoting, while simultaneously recording stepping movement, striatal cellular calcium dynamics and local field potentials (LFPs). We found that 10 Hz, but not 145 Hz stimulation prominently entrained striatal LFPs. Even though sensory stimulation at both frequencies promoted locomotion and desynchronized striatal network, only 10 Hz stimulation enhanced the delta rhythmicity of stepping movement and strengthened the coupling between stepping and striatal LFP delta and beta oscillations. These results demonstrate that higher frequency sensory stimulation can modulate lower frequency dorsal striatal neural dynamics and improve stepping rhythmicity, highlighting the translational potential of non-invasive beta-frequency sensory stimulation for improving gait.

neuroscience↗

bioRxiv2024

Development of RT-RPA-based point-of-care tests for epidemic arthritogenic alphaviruses

Chikungunya (CHIKV), onyong-nyong (ONNV), and Mayaro (MAYV) viruses are transmitted by mosquitoes and known to cause a debilitating arthritogenic syndrome. These alphaviruses have emerged and re-emerged, leading to outbreaks in tropical and subtropical regions of Asia, South America, and Africa. Despite their prevalence, there persists a critical gap in the availability of sensitive and virus-specific point-of-care (POC) diagnostics. Traditional immunoglobulin-based tests such as enzyme-linked immunosorbent assay (ELISAs) often yield cross-reactive results due to the close genetic relationship between these viruses. Molecular diagnostics such as quantitative polymerase chain reaction (qPCR) offer high sensitivity but are limited by the need for specialized laboratory equipment. Recombinase polymerase amplification (RPA), an isothermal amplification method, is a promising alternative to qPCR, providing rapid results with minimal equipment requirements. Here, we report the development and validation of three virus-specific RPA-based POC tests for CHIKV, ONNV, and MAYV. These tests demonstrated both speed and sensitivity, capable of detecting 10 viral copies within 20 minutes of amplification, without exhibiting cross-reactivity. Furthermore, we evaluated the clinical potential of these tests using serum and tissue samples from CHIKV, ONNV, and MAYV-infected mice, as well as CHIKV-infected human patients. We demonstrate that the RPA amplicons derived from the patient samples can be sequenced, enabling cost-effective molecular epidemiological studies. Our findings highlight the significance of these rapid and specific POC diagnostics in improving the early detection and management of these arboviral infections.

microbiology↗

bioRxiv2024

Antibody responses in Klebsiella pneumoniae bloodstream infection: a cohort study

BackgroundKlebsiella pneumonia (Kpn) is the fourth leading cause of infection-related deaths globally, yet little is known about human antibody responses to invasive Kpn. In this study, we sought to determine whether the O-specific polysaccharide (OPS) antigen, a vaccine candidate, is immunogenic in humans with Kpn bloodstream infection (BSI). We also sought to define the cross-reactivity of human antibody responses among structurally related Kpn OPS subtypes and to assess the impact of capsule production on OPS-targeted antibody binding and function. MethodsWe measured plasma antibody responses to OPS (and MrkA, a fimbrial protein) in a cohort of patients with Kpn BSI and compared these with controls, including a cohort of healthy individuals and a cohort of individuals with Enterococcus BSI. We performed flow cytometry to measure the impact of Kpn capsule production on whole cell antibody binding and complement deposition, utilizing patient isolates with variable levels of capsule production and isogenic capsule-deficient strains derived from these isolates. FindingsWe enrolled 69 patients with Kpn BSI. Common OPS serotypes accounted for 57/69 (83%) of infections. OPS was highly immunogenic in patients with Kpn BSI, and peak OPS-IgG antibody responses in patients were 10 to 30-fold higher than antibody levels detected in healthy controls, depending on the serotype. There was significant cross-reactivity among structurally similar OPS subtypes, including the O1v1/O1v2, O2v1/O2v2 and O3/O3b subtypes. Physiological amounts of capsule produced by both hyperencapsulated and non-hyperencapsulated Kpn significantly inhibited OPS-targeted antibody binding and function. InterpretationOPS was highly immunogenic in patients with Kpn BSI, supporting its potential as a candidate vaccine antigen. The strong cross-reactivity observed between similar OPS subtypes in humans with Kpn BSI suggests that it may not be necessary to include all subtypes in an OPS-based vaccine. However, these observations are tempered by the fact that capsule production, even in non-highly encapsulated strains, has the potential to interfere with OPS antibody binding. This may limit the effectiveness of vaccines that exclusively target OPS. FundingNational Institute of Allergy and Infectious Diseases at the National Institutes of Health. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSDespite the potential of O-specific polysaccharide (OPS) as a vaccine antigen against Klebsiella pneumoniae (Kpn), the immunogenicity of OPS in humans remains largely unstudied, creating a significant knowledge gap with regard to vaccine development. A search of PubMed for publications up to March 18, 2024, using the terms "Klebsiella pneumoniae" and "O-specific polysaccharide" or "O-antigen" or "lipopolysaccharide" revealed no prior studies addressing OPS antibody responses in humans with Kpn bloodstream infections (BSI). One prior study1 evaluated antibody response to a single lipopolysaccharide (which contains one subtype of OPS) in humans with invasive Kpn infection; however, in this study OPS typing of the infecting strains and target antigen were not described. Added value of this studyOur investigation into OPS immunogenicity in a human cohort marks a significant advance. Analyzing plasma antibody responses in 69 patients with Kpn BSI, we found OPS to be broadly immunogenic across all the types and subtypes examined, and there was significant cross-reactivity among structurally related OPS antigens. We also demonstrated that Kpn capsule production inhibit OPS antibody binding and the activation of complement on the bacterial surface, even in classical Kpn strains expressing lower levels of capsule. Implications of all the available evidenceWhile the immunogenicity and broad cross-reactivity of OPS in humans with Kpn BSI suggests it is a promising vaccine candidate, the obstruction of OPS antibody binding and engagement by physiologic levels of Kpn capsule underscores the potential limitations of an exclusively OPS-antigen based vaccine for Kpn. Our study provides insights for the strategic development of vaccines aimed at combating Kpn infections, an important antimicrobial resistant pathogen.

microbiology↗

bioRxiv2024

Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina

A standard circuit motif in sensory systems is the pooling of sensory information from an upstream neuronal layer. A downstream neuron thereby collects signals across different locations in stimulus space, which together compose the neurons receptive field. In addition, nonlinear transformations in the signal transfer between the layers give rise to functional subunits inside the receptive field. For ganglion cells in the vertebrate retina, for example, receptive field subunits are thought to correspond to presynaptic bipolar cells. Identifying the number and locations of subunits from the stimulus-response relationship of a recorded ganglion cell has been an ongoing challenge in order to characterize the retinas functional circuitry and to build computational models that capture nonlinear signal pooling. Here we present a novel version of spike-triggered non-negative matrix factorization (STNMF), which can extract localized subunits in ganglion-cell receptive fields from recorded spiking responses under spatiotemporal white-noise stimulation. The method provides a more than 100-fold speed increase compared to a previous implementation, which can be harnessed for systematic screening of hyperparameters, such as sparsity regularization. We demonstrate the power and flexibility of this approach by analyzing populations of ganglion cells from salamander and primate retina. We find that subunits of midget as well as parasol ganglion cells in the marmoset retina form separate mosaics that tile visual space. Moreover, subunit mosaics show alignment with each other for ON and OFF midget as well as for ON and OFF parasol cells, indicating a spatial coordination of ON and OFF signals at the bipolar-cell level. Thus, STNMF can reveal organizational principles of signal transmission between successive neural layers, which are not easily accessible by other means.

neuroscience↗

bioRxiv2024

Modeling spatial contrast sensitivity in responses of primate retinal ganglion cells to natural movies

Retinal ganglion cells, the output neurons of the vertebrate retina, often display nonlinear summation of visual signals over their receptive fields. This creates sensitivity to spatial contrast, letting the cells respond to spatially structured visual stimuli even when no net change in overall illumination of the receptive field occurs. Yet, computational models of ganglion cell responses are often based on linear receptive fields, and typical nonlinear extensions, which separate receptive fields into nonlinearly combined subunits, are often cumbersome to fit to experimental data. Previous work has suggested to model spatial-contrast sensitivity in responses to flashed images by combining signals from the mean and variance of light intensity inside the receptive field. Here, we extend and adjust this spatial contrast model for application to spatiotemporal stimulation and explore its performance on spiking responses that we recorded from ganglion cells of marmosets under artificial and naturalistic movies. We show how the model can be fitted to experimental data and that it outperforms common models with linear spatial integration to different degrees for different types of ganglion cells. Finally, we use the model framework to infer the cells spatial scale of nonlinear spatial integration. Our work shows that the spatial contrast model can capture aspects of nonlinear spatial integration in the primate retina with only few free parameters. The model can be used to assess the cells functional properties under natural stimulation and provides a simple-to-obtain benchmark for comparison with more detailed nonlinear encoding models. Author SummaryOur visual experience depends on the retinas remarkable ability to detect light patterns and contrast in the world around us. Retinal ganglion cells, the output neurons of the retina, modulate their activity based on signals within small, specific regions of the visual scene, called their receptive fields. But many cells do not only encode overall brightness, summed linearly across the receptive field, but are also sensitive to local spatial contrast, that is, variations in brightness within the receptive field. Computational models that account for this nonlinear spatial integration exist, but require large amounts of data and are challenging to fit. We therefore developed the spatial contrast model, which takes a simple measure of light-intensity variations as an input, and tested it on measured responses of primate retinal ganglion cells to both artificial and naturalistic movies. The model substantially outperformed standard models with linear receptive fields, despite having only one additional tunable parameter. Furthermore, we used the model to investigate the spatial scale at which the cells integrate spatial contrast and found striking consistency across cell types. The spatial contrast model thus offers a practical tool for capturing retinal stimulus encoding and a simple-to-obtain benchmark for modeling nonlinear spatial integration.

neuroscience↗

bioRxiv2024

Convolutional neural network models of the primate retina reveal adaptation to natural stimulus statistics

Understanding the nonlinear encoding mechanisms of retinal ganglion cells (RGCs) in response to various visual stimuli presents a central challenge in neuroscience, driving the development of increasingly complex predictive models. Here, we systematically evaluate linear-nonlinear (LN) models - applying various regularization techniques - and convolutional neural networks (CNNs) of increasing depth, to predict RGC responses to white noise and natural movies. Our analysis includes publicly available datasets from marmoset and salamander retinas. We demonstrate that LN models, when equipped with appropriate inductive biases, can achieve robust predictive performance on neural responses to both white noise and natural movie stimuli. The optimal inductive biases vary substantially across datasets and stimulus types, indicating that the LN models performance is susceptible to these choices. This warrants care when using LN models as baselines: their performance is not fixed, and inappropriate design choices can lead to "unfair" comparisons. However, even in the optimal inductive bias scenario, CNNs consistently outperform LN models across conditions, confirming the advantage derived from their nonlinear representation capacity. Investigating cross-stimulus generalization, we observe that models trained on white noise generalize better to natural movies than vice versa. Notably, LN models exhibit a smaller performance gap between in-domain and cross-domain predictions compared to CNNs, suggesting that the nonlinear processing captured by CNNs is more stimulus-specific. Overall, this study provides valuable benchmarks and methodological insights for neuroscientists designing predictive models of retinal encoding.

neuroscience↗

bioRxiv2024

Discovery of novel compounds and target mechanisms using a high throughput, multiparametric phenotypic screen in a human neuronal model of Tuberous Sclerosis

Tuberous sclerosis complex (TSC) is a rare genetic disorder caused by mutations in the mTOR pathway genes TSC1 or TSC2. TSC can affect multiple organs including the brain, and most patients (75-90%) present with seizures during early childhood and intractable epilepsy throughout life. mTOR inhibitors, part of the current standard of care, lack the optimal characteristics to fully address patient phenotypes. Here, we report on the application of our all-optical electrophysiology platform for phenotypic screening in a human neuronal model of TSC. We used CRISPR/Cas9-isogenic TSC2-/- iPS cell lines to identify disease-associated changes to neuronal morphology, transcript expression and neuronal excitability. We established a robust multiparametric electrophysiological phenotype which we then validated in TSC patient-derived neurons. We used this phenotype to conduct a screen of [~]30,000 small molecule compounds in human iPS cell-derived neurons and identified chemical scaffolds that rescued the functional TSC disease parameters. Confirmed hits may act via different mechanisms than direct mTOR pathway inhibition. This strategy provides molecular starting points for therapeutic development in TSC and a framework for phenotype discovery and drug screening in other neurological disorders.

neuroscience↗

bioRxiv2024

Inhibition of Indirect Pathway Activity Causes Abnormal Decision-Making In a Mouse Model of Impulse Control Disorder in Parkinson's Disease

Healthy action selection relies on the coordinated activity of striatal direct and indirect pathway neurons. In Parkinsons disease (PD), in which loss of midbrain dopamine neurons is associated with progressive motor and cognitive deficits, this coordination is disrupted. Dopamine replacement therapy can remediate motor symptoms, but can also cause impulse control disorder (ICD), which is characterized by pathological gambling, hypersexuality, and/or compulsive shopping. The cellular and circuit mechanisms of ICD remain unknown. Here we developed a mouse model of PD/ICD, in which ICD-like behavior was assayed with a delay discounting task. We found that in parkinsonian mice, the dopamine agonist pramipexole drove more pronounced delay discounting, as well as disrupted firing in both direct and indirect pathway neurons. We found that chemogenetic inhibition of indirect pathway neurons in parkinsonian mice drove similar phenotypes. Together, these findings provide a new mouse model and insights into ICD pathophysiology.

neuroscience↗

bioRxiv2023

Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina

Spatially nonlinear stimulus integration by retinal ganglion cells lies at the heart of various computations performed by the retina. It arises from the nonlinear transmission of signals that ganglion cells receive from bipolar cells, which thereby constitute functional subunits within a ganglion cells receptive field. Inferring these subunits from recorded ganglion cell activity promises a new avenue for studying the functional architecture of the retina. This calls for efficient methods, which leave sufficient experimental time to leverage the acquired knowledge. Here, we combine concepts from super-resolution microscopy and computed tomography and introduce super-resolved tomographic reconstruction (STR) as a technique to efficiently stimulate and locate receptive field subunits. Simulations demonstrate that this approach can reliably identify subunits across a wide range of model variations, and application in recordings of primate parasol ganglion cells validates the experimental feasibility. STR can potentially reveal comprehensive subunit layouts within less than an hour of recording time, making it ideal for online analysis and closed-loop investigations of receptive field substructure in retina recordings.

neuroscience↗