Biology subjects

Lynch, G.

Publications and source records attributed to Lynch, G..

12 recordsLinked to original sources

bioRxiv2026

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

neuroscience↗

bioRxiv2026

Early life Oxytocin treatment Attenuates Seizure Susceptibility in Male, but not Female, Fmr1-KO Mice

Fragile X syndrome (FXS) is the leading inherited cause of intellectual disability, and is frequently accompanied by seizures. Early-life treatment with the hormone oxytocin (OXT) improves social behavior and cognitive function in rodent models of autism with intellectual disability, including FXS, but potential OXT treatment effects on seizure susceptibility have not been evaluated. Here we tested, in both sexes, if intranasal OXT (iOXT) or saline (iSAL) during the second postnatal week reduces audiogenic seizures (AGS) in the Fmr1-Knockout (KO) mouse model of FXS. OXT given daily from postnatal day (P) 7 to P13 significantly reduced the incidence and severity of AGS and the latency to seize in adult male Fmr1-KOs. Female KOs exhibited less severe seizures that were unaffected by treatment. Wild type mice did not exhibit AGS independent of treatment. To test if antiepileptic effects of iOXT are age-dependent, a separate cohort received iOXT daily from P30 to P36. Male KOs receiving later treatments exhibited robust seizures that were comparable between OXT- and SAL-treatment groups, suggesting that OXTs enduring antiepileptic effects are confined to early postnatal treatments. Tests of acute OXT effects in adulthood demonstrated an attenuation of male Fmr1-KO AGS at testing 30-60 min and 1 day post-treatment but these effects were not evident 15 days later. These findings reveal marked sex differences in the propensity for audiogenic seizures in Fmr1-KO mice and demonstrate that early-life OXT treatment mitigates seizure susceptibility in males FXS model mice.

neuroscience↗

bioRxiv2025

Cocaine Blocks Cholinergic Activity in the Medial Habenula Prior to But Not After Induced Preference for the Drug

Descending projections from the medial habenula potently influence brainstem systems associated with reward and mood. Relatedly, the ventral, cholinergic segment of the nucleus has been linked to nicotine and cocaine addiction. Here we report that cocaine has no effect on baseline firing in the ventral medial habenula but entirely blocks the self-sustained activity initiated by endogenous acetylcholine. This effect was not altered by antagonists to dopamine receptors and thus presumably reflects a direct action on cholinergic receptors. Remarkably, cocaine had no effect on endogenous cholinergic activity in mice that had been extinguished from an induced cocaine preference. In all, the drug has potent effects, albeit through an exotic mode of action, on the medial habenula and these are eliminated by prior experience with the drug. These results describe a novel target for cocaine that is plausibly related to the psychological effects of the drug, and an unexpected consequence of earlier use.

neuroscience↗

bioRxiv2025

The characteristic of epithelial-specific phenotypes and immunosuppressive microenvironment in the context of tumour budding in colorectal cancer

BackgroundTumour budding (TB), defined as a small cluster of up to four cells at the invasive front of the tumour, is a well-established independent and robust prognostic biomarker in colorectal cancer (CRC). This is strongly associated with adverse clinicopathological features and poor survival outcomes. Despite its clinical relevance, the precise underlying mechanism responsible for TB phenomenon remains unclear. MethodsMulti-omic approaches from bulk, regional GeoMx and Spatial Molecular Imager (SMI) RNA were used to identify the underlying mechanism of TB and its possible correlation with tumour microenvironment (TME) in CRC tissue. The results were validated using immunohistochemistry (IHC) and multiplex immunofluorescence (mIF) staining. ResultsPatients with high TB experience worse outcomes and associate with adverse clinical factors across two independent CRC cohorts. Bulk and regional RNA expression analyses reveal that tumours with high TB are significantly enriched for TNF- and TGF-{beta} signatures in both cohorts. Single cell CosMx SMI analysis confirmed TB cells exhibit higher expression of these signatures than adjacent invasive edge tumour cells. Elevated cyclinD1 expression was also observed within TB, and high cyclinD1 levels tend to experience poorer CRC prognosis. Furthermore, regional bulk RNA expression within the non-tumour (PanCK-) invasive edge areas demonstrated that tumours exhibiting high TB revealed the significantly differential expressions of immune-related genes (e.g. CD3, NKG7, IL6, CXCR6, CD47, IFNAR1 and VSIR). Single cell CosMx SMI analysis revealed that cancer-associated fibroblasts (CAFs) were physically the closest cells to TB cells. This spatial proximity was confirmed at the protein level using mIF, where the distance from TB to CD68+ macrophages predicted significantly poorer CRC outcomes. ConclusionThis multi-omic study confirms the prognostic significance of TB in CRC patients across two independent cohorts. Our findings highlight that TNF- and TGF-{beta} signalling play a crucial role in budding cells development by regulating cyclinD1. Furthermore, the transcriptomic analysis reveals an immunosuppressive niche characterised by reduced immune activity and close spatial interactions with CAFs and macrophages Ultimately, this study provides valuable insight into TBs underlying mechanism and its complex interactions within the TME. This could provide a foundation for developing targeted therapeutic strategies in CRC.

cancer biology↗

bioRxiv2024

Early-life Oxytocin Rescues Hippocampal Synaptic Plasticity and Episodic Memory in a Mouse Model of Fragile X Syndrome

Cognitive disabilities including impairments to episodic memory are debilitating features of autism spectrum disorder (ASD). Here we report that early-life treatment with oxytocin (OXT) fully restores episodic memory and associated synaptic plasticity in a rodent model of an ASD. Fmr1-knockout (KO) mice -- which mimic the single gene mutation in Fragile X Syndrome -- failed to encode three basic elements of an episode (identity, location, and temporal order) during a first time, unrewarded encounter with a set of cues. Intranasal administration of OXT during the second postnatal week eliminated each of these impairments in mice tested in adulthood. OXT treatment during the second, but not fifth, postnatal week also corrected pronounced defects in two distinct forms of hippocampal Long-Term Potentiation (LTP). Rescue of LTP in lateral perforant path (LPP) to dentate gyrus synapses was linked to recovery of NMDAR-gated synaptic responses, which are otherwise profoundly reduced in the mutant LPP. LTP induced by a threshold theta burst stimulation protocol in CA3-CA1 synapses was severely impaired in adult Fmr1-KOs as was a previously unreported post-induction growth phase for potentiation. Both effects were restored in adult Fmr1-KOs given early OXT treatment. Infusion of OXT into adult Fmr1-KO hippocampal slices normalized LTP in CA1 but had no effect on the defective potentiation (or NMDAR-mediated EPSCs) at LPP-dentate gyrus synapses. These results show that severe, autism-related defects in cognition critical to memory, as evident in a rodent model, are reversible and that an early-life therapeutic intervention can effect an enduring restoration of function.

neuroscience↗

bioRxiv2024

Metabotropic NMDA Receptor Signaling Contributes to Sex Differences in Synaptic Plasticity and Episodic Memory

Men generally outperform women on encoding spatial components of episodic memory whereas the reverse holds for semantic elements. Here we show that female mice outperform males on tests for non-spatial aspects of episodic memory ("what", "when"), suggesting that the human findings are influenced by neurobiological factors common to mammals. Analysis of hippocampal synaptic plasticity mechanisms and encoding revealed unprecedented, sex-specific contributions of non-classical metabotropic NMDA receptor (NMDAR) functions. While both sexes used non-ionic NMDAR signaling to trigger actin polymerization needed to consolidate long-term potentiation (LTP), NMDAR GluN2B subunit antagonism blocked these effects in males only and had the corresponding sex-specific effect on episodic memory. Conversely, blocking estrogen receptor alpha eliminated metabotropic stabilization of LTP and episodic memory in females only. The results show that sex differences in metabotropic signaling critical for enduring synaptic plasticity in hippocampus have significant consequences for encoding episodic memories.

neuroscience↗

bioRxiv2023

Input / Output Relationships for the Primary Hippocampal Circuit.

The hippocampus is likely the most studied brain region but little is known about signal throughput -- the simplest, yet most essential of circuit operations -- across its multiple stages from perforant path input to CA1. Here we report that single pulse stimulation of the lateral perforant path (LPP) produces a two-part CA1 response generated by projections to CA3 ("direct path") and the dentate gyrus ("indirect path"). The latter was by far the more potent in driving CA1 output because it engaged the massive recurrent collateral system and elicited a series of fEPSPs and spikes in CA3. The mobilization time for this stereotyped sharp wave-like response resulted in surprisingly slow throughput. The circuit did not convey high frequency LPP trains but transmitted single pulses, or bursts of pulses separated by the period of the theta wave. During these activation patterns CA1 output faithfully reproduced a version of the LPP input. We conclude that the basic hippocampal circuit, despite its considerable complexity, has a default mode in which select cortical signals are reliably transferred to output stations. Significance statementThe hippocampus, a brain structure synonymous with episodic memory, is one of the most studied brain regions in neuroscience today. However, despite this intense interest, surprisingly little is known about how signals are transformed and processed by the hippocampal circuit. As a result, there are currently no "bottom up" hypotheses about how the structure supports its physiological function(s). Here, we use a novel brain slice preparation to describe the signal transformations occurring across the primary hippocampal circuit. The results identify novel circuit operations that challenge the notion of the tri-synaptic circuit and provide evidence for frequency-dependent filters that are critical for determining signal throughput. These findings provide an initial link between basic circuit function(s) and events recorded in behaving animals.

neuroscience↗

bioRxiv2022

Signal Transformations and New Timing Rules of Hippocampal CA3 to CA1 Synapses

The synapse is the fundamental unit of communication in the nervous system. Determining how information is transferred across the synaptic interface is one of the most complex endeavors in neuroscience, owing to the large number of contributing factors and events. An approach to solving this problem involves collapsing across these complexities to derive concise mathematical formulas that fully capture the governing dynamics of synaptic transmission. We investigated the feasibility of deriving such a formula - an input-output transformation function for the CA3 to CA1 node of the hippocampus -- using the Volterra expansion technique for nonlinear system identification. The entirety of the field EPSP in the apical dendrites of mouse brain slices was described with >94% accuracy by a 2nd order equation that captured the linear and nonlinear influence of past inputs on current outputs. This function generalized to cases not included in its derivation and uncovered previously undetected timing rules. The basal dendrites expressed a substantially different transfer function and evidence was obtained that, unlike the apical system, a 3rd order system or higher will be needed for complete characterization. Collectively, these results describe a readily implemented and unusually sensitive means for evaluating the effects of pharmacological treatments and disease related conditions on synaptic dynamics. At scale, the approach will also provide information needed for the construction of biologically realistic models of brain networks.

neuroscience↗

bioRxiv2021

Endogenous Syngap1 Alpha Splice Forms Promote Cognitive Function and Seizure Protection

Loss-of-function variants in SYNAGP1 cause a developmental encephalopathy defined by cognitive impairment, autistic features, and epilepsy. SYNGAP1 splicing leads to expression of distinct functional protein isoforms. Splicing imparts multiple cellular functions of SynGAP proteins through coding of distinct C-terminal motifs. However, it remains unknown how these different splice sequences function in vivo to regulate neuronal function and behavior. Reduced expression of SynGAP-1/2 C-terminal splice variants in mice caused severe phenotypes, including reduced survival, impaired learning, and reduced seizure latency. In contrast, upregulation of 1/2 expression improved learning and increased seizure latency. Mice expressing 1-specific mutations, which disrupted SynGAP cellular functions without altering protein expression, promoted seizure, disrupted synapse plasticity, and impaired learning. These findings demonstrate that endogenous SynGAP isoforms with 1/2 spliced sequences promote cognitive function and impart seizure protection. Regulation of SynGAP- expression or function may be a viable therapeutic strategy to broadly improve cognitive function and mitigate seizure.

neuroscience↗

bioRxiv2020

Splicing of the SynGAP Carboxyl-Terminus Enables Isoform-Specific Tuning of NMDA Receptor Signaling Linked to Cognitive Function

SynGAP-1 is a splice variant of the neurodevelopmental disorder risk gene, SYNGAP1/Syngap1. 1 encodes the C-terminal PDZ binding motif (PBM) that promotes liquid-liquid phase separation, a candidate process for postsynaptic density organization within excitatory synapses. However, it remains unknown how the endogenous SynGAP PBM regulates synapse properties and related cognitive functions. We found that a major PBM function in mice is to limit the mobility of SynGAP-1 in response to NMDA receptor activation. Genetic disruption of the PBM increased SynGAP-1 mobility to levels consistent with other non-PBM-containing C-terminal isoforms. This resulted in a lowering of the threshold for NMDA receptor-dependent signaling required for plasticity, leading to aberrant strengthening of excitatory synapses in spontaneously active neurons. PBM-deficient animals also exhibited a lower seizure threshold, disrupted LTP, and impaired cognition. Thus, the PBM enables isoform-specific SynGAP gating of NMDA receptor function, a mechanism linking synaptic signaling dynamics to network excitability and cognition.

neuroscience↗

bioRxiv2019

Acquisition of Temporal Order Involves a Reverberating Network in Hippocampal Field CA3

Here we report that hippocampal field CA3 maintains self-sustained activity for remarkable periods following a brief input and that this effect is extremely sensitive to minor perturbations. Using novel behavioral tests, that as with human episodic learning do not involve training or explicit rewards, we show that partial silencing of the network in mice blocks acquisition of temporal order, but not the identity or location, of odors. These results suggest a solution to the question of how hippocampus adds time to episodic memories.

neuroscience↗

bioRxiv2018

UBE3A-mediated p18/LAMTOR1 ubiquitination and degradation regulate mTORC1 activity and synaptic plasticity

Accumulating evidence indicates that the lysosomal Ragulator complex is essential for full activation of the mechanistic target of rapamycin complex 1 (mTORC1). Abnormal mTORC1 activation has been implicated in several developmental neurological disorders, including Angelman syndrome (AS), which is caused by maternal deficiency of the ubiquitin E3 ligase UBE3A. Here we report that Ube3a regulates mTORC1 signaling by targeting p18, a subunit of the Ragulator. Ube3a ubiquinates p18, resulting in its proteasomal degradation, and Ube3a deficiency in hippocampus of AS mice results in increased lysosomal localization of p18 and other members of the Ragulator-Rag complex, such as RagA, and increased mTORC1 activity. P18 down-regulation by siRNA or shRNA in hippocampal CA1 neurons of AS mice reduces elevated mTORC1 activity and improves long-term potentiation (LTP) and dendritic spine maturation. Our results indicate that Ube3a-mediated regulation of p18 and subsequent mTORC1 signaling is critical for typical synaptic plasticity and dendritic spine development.

neuroscience↗