Biology subjects

Lam, S.

Publications and source records attributed to Lam, S..

34 records · Page 2Linked to original sources

bioRxiv2022

In vivo spatiotemporal dynamics of astrocyte reactivity following neural electrode implantation

Brain computer interfaces (BCIs), including penetrating microelectrode arrays, enable both recording and stimulation of neuronal cells. However, device implantation inevitably causes injury to brain tissue and induces a foreign body response, leading to reduced recording performance and stimulation efficacy. Astrocytes in the healthy brain play multiple roles including regulating energy metabolism, homeostatic balance, transmission of neural signals, and neurovascular coupling. Following an insult to the brain, they are activated and observed to gather around the site of injury. These reactive astrocytes have been regarded as one of the main contributors to the formation of a glial scar which affects the performance of microelectrode arrays. This study investigates the dynamics of astrocytes within the first 2 weeks after implantation of an intracortical microelectrode into the mouse brain using two-photon microscopy. From our observation astrocytes are highly dynamic during this period, exhibiting patterns of process extension, soma migration, morphological activation, and device encapsulation that are spatiotemporally distinct from other glial cells, such as microglia or oligodendrocyte precursor cells. This detailed characterization of astrocyte reactivity will help to better understand the tissue response to intracortical devices and lead to the development of more effective intervention strategies to improve the functional performance neural interfacing technology.

bioengineering↗

bioRxiv2022

Insulin Receptor Loss Impairs Mammary Tumorigenesis in Mice

Breast cancer (BC) prognosis and outcome are adversely affected by obesity. Hyperinsulinemia, common in obese state, is associated with higher risk of death and recurrence in BC. Up to 80% of breast cancers overexpress the insulin receptor (INSR), which correlates with worse prognosis. INSR role in mammary tumorigenesis was tested by generating MMTV-driven polyoma middle T (PyMT) and ErbB2/Her2 BC mouse models, respectively, with coordinate mammary epithelium-restricted deletion of INSR. In both models, deletion of either one or both copies of INSR led to a marked delay in tumor onset and burden. Longitudinal phenotypic characterization of mouse tumours and cells revealed that INSR deletion impacted tumour initiation, not progression and metastasis. INSR upheld a bioenergetic phenotype in non-transformed mammary epithelial cells, independent of its kinase activity. Similarity of phenotypes elicited by deletion of one or both copies of INSR suggest a dose-dependent threshold for INSR impact on mammary tumorigenesis.

cancer biology↗

bioRxiv2022

Double knockout CRISPR screen in cancer resistance to T cell cytotoxicity

Immunotherapy has transformed cancer treatments; however, a large fraction of patients encounter resistance. Such resistance is mediated by complex factors, often involving interactions between multiple genes. Thus, it is crucially important to identify genetic interactions between genes that are significantly mutated in cancer patients and those involved in immune responses, ideally the ones that currently have chemical compounds for direct targeting. To systematically interrogate such genetic interactions that mediate cancer cells response to T cell killing, we designed an asymmetric CRISPR/Cas9 dual perturbation library targeting the matched combinations between significantly mutated tumor suppressors and immune resistance genes. We performed a combinatorial double knockout screen on 1,159 gene pairs and identified those where joint loss-of-function renders altered cellular response to T cell cytotoxicity. With individual double knockout constructs we validated these genetic interactions including Jak1-Trp53, Jak1-Kmt2d, and Ifngr1-Kmt2d. Interactions between significantly mutated tumor suppressors and potentially druggable immune resistance genes may offer insights on potential new concepts of how to target clinically relevant cancer mutations with currently available agents. This study also provides a technology platform and an asymmetric CRISPR double knockout library for interrogating genetic interactions between cancer mutations and immune resistance pathways under various settings.

genomics↗

bioRxiv2021

T cell receptor repertoire signatures associated with COVID-19 severity

T cell receptor (TCR) repertoires are critical for antiviral immunity. Determining the TCR repertoires composition, diversity, and dynamics and how they change during viral infection can inform the molecular specificity of viral infection such as SARS-CoV-2. To determine signatures associated with COVID-19 disease severity, here we performed a large-scale analysis of over 4.7 billion sequences across 2,130 TCR repertoires from COVID-19 patients and healthy donors. TCR repertoire analyses from these data identified and characterized convergent COVID-19 associated CDR3 gene usages, specificity groups, and sequence patterns. T cell clonal expansion was found to be associated with upregulation of T cell effector function, TCR signaling, NF-kB signaling, and Interferon-gamma signaling pathways. Machine learning approaches accurately predicted disease severity for patients based on TCR sequence features, with certain high-power models reaching near-perfect AUROC scores across various predictor permutations. These analyses provided an integrative, systems immunology view of T cell adaptive immune responses to COVID-19.

bioinformatics↗

bioRxiv2021

Anisotropic interaction and motion states of locusts in a hopper band

Swarming locusts present a quintessential example of animal collective motion. Juvenile locusts march and hop across the ground in coordinated groups called hopper bands. Composed of up to millions of insects, hopper bands exhibit aligned motion and various collective structures. These groups are well-documented in the field, but the individual insects themselves are typically studied in much smaller groups in laboratory experiments. We present the first trajectory data that detail the movement of individual locusts within a hopper band in a natural setting. Using automated video tracking, we derive our data from footage of four distinct hopper bands of the Australian plague locust, Chortoicetes terminifera. We reconstruct nearly twenty-thousand individual trajectories composed of over 3.3 million locust positions. We classify these data into three motion states: stationary, walking, and hopping. Distributions of relative neighbor positions reveal anisotropies that depend on motion state. Stationary locusts have high-density areas distributed around them apparently at random. Walking locusts have a low-density area in front of them. Hopping locusts have low-density areas in front and behind them. Our results suggest novel insect interactions, namely that locusts change their motion to avoid colliding with neighbors in front of them.

animal behavior and cognition↗

bioRxiv2021

The miR-124-AMPAR pathway connects polygenic risks with behavioral changes shared between schizophrenia and bipolar disorder

Schizophrenia (SZ) and bipolar disorder (BP) are highly heritable major psychiatric disorders that share a substantial portion of genetic risk as well as their clinical manifestations. This raises a fundamental question of whether, and how, common neurobiological pathways translate their shared polygenic risks into shared clinical manifestations. The present study shows the miR-124-AMPAR pathway as a key common neurobiological mediator that connects polygenic risks with behavioral changes shared between these two psychotic disorders. We discovered upregulation of miR-124 in biopsied neuronal cells and postmortem prefrontal cortex from both SZ and BP patients, implying its role not only as a biomarker, but also as a pathophysiological mediator. Intriguingly, the upregulation is associated with the polygenic risks shared between these two disorders. Seeking mechanistic dissection, we generated a mouse model that upregulates miR-124 in the medial prefrontal cortex, which includes brain regions homologous to sub-regions of the human prefrontal cortex. We demonstrated that upregulation of miR-124 increases GRIA2-lacking calcium permeable-AMPARs and perturbs AMPAR-mediated excitatory synaptic transmission, leading to deficits in the behavioral dimensions shared between SZ and BP.

neuroscience↗

bioRxiv2021

N-dihydrogalactochitosan reduces mortality in a lethal mouse model of SARS-CoV-2

The rapid emergence and global dissemination of SARS-CoV-2 that causes COVID-19 continues to cause an unprecedented global health burden resulting in nearly 7 million deaths. While multiple vaccine countermeasures have been approved for emergency use, additional treatments are still needed due to sluggish vaccine rollout, vaccine hesitancy, and inefficient vaccine-mediated protection. Immunoadjuvant compounds delivered intranasally can guide non-specific innate immune responses during the critical early stages of viral replication, reducing morbidity and mortality. N- dihydrogalactochitosan (GC) is a novel mucoadhesive immunostimulatory polymer of {beta}- 0-4-linked N-acetylglucosamine that is solubilized by the conjugation of galactose glycans with current applications as a cancer immunotherapeutic. We tested GC as a potential countermeasure for COVID-19. GC was well-tolerated and did not produce histopathologic lesions in the mouse lung. GC administered intranasally before and after SARS-CoV-2 exposure diminished morbidity and mortality in humanized ACE2 receptor expressing mice by up to 75% and reduced infectious virus levels in the upper airway. Fluorescent labeling of GC shows that it is confined to the lumen or superficial mucosa of the nasal cavity, without involvement of adjacent or deeper tissues. Our findings demonstrate a new application for soluble immunoadjuvants such as GC for preventing disease associated with SARS-CoV-2 and may be particularly attractive to persons who are needle-averse. IMPORTANCEThe ongoing COVID-19 pandemic necessitates new approaches to reduce disease caused by SARS-CoV-2. We tested the immunoadjuvant N-dihydrogalactochitosan (GC), used previously as an immunostimulant for tumor therapy and adjuvant for viral vaccines, as a potential COVID-19 countermeasure. When GC was administered before and after inoculation of a lethal dose of SARS-CoV-2 into the nose of humanized mice expressing an entry receptor for the virus, fewer mice showed weight loss and died compared to mice that received only the vehicle but no GC. GC-treated mice also had lower levels of infectious SARS-CoV-2 in their upper airway. These results suggest that GC may be a candidate to prevent or treat COVID-19. Single Sentence SummaryThe immunoadjuvant N-dihydrogalactochitosan diminishes SARS-CoV-2 disease in humanized ACE2 mice, representing a new countermeasure against COVID-19.

microbiology↗

bioRxiv2021

Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer's and Parkinson's diseases

Neurodegenerative diseases (NDDs), including Alzheimers (AD) and Parkinsons diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analyse transcriptomic data from AD and PD patients, and stratify these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identify retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrate that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.

systems biology↗

bioRxiv2021

A deep learning approach to neurite prediction in high throughput fluorescence imaging

Changes to neuronal morphology and loss of neurites and synaptic connections can be an important early indicator of neurological diseases, and a pathognomonic sign of neurodevelopmental disorders. These changes are typically detectable by microscopy in cell culture or histological samples, but quantification can be challenging. The neurites extending from cell soma can be quite thin, dim, overlapping and complex, making them laborious to trace manually and difficult to annotate and quantify computationally or automatically. Moreover, the tools available to aid this aim are limited in their capacity to generalize to high throughput image acquisition such as time-lapse or longitudinal imaging, where imaging conditions can change dramatically over the course of the experiment. In order to facilitate neurite quantification, we developed a deep learning (DL) neurite annotation prediction algorithm (NAPA) to predict the structure and length of neurites. NAPA overcomes experimental variation inherent to fluorescence imaging by learning more broader features that are important for neurite recognition. Based on a dataset with partial annotation, NAPA generated predictions on several unannotated datasets, and was able to capture differences between disease and control conditions. We also defined a sequence of steps to generate custom models with a small number of annotation inputs, and extended the predictions to a 3D tissue sample and longitudinal imaging. With this algorithm we developed an approach to quantify neurites with an accuracy that nears and sometimes exceeds human curation, in 1/100th of the time. This approach makes accurate analysis of large or longitudinal datasets feasible across a broad range of datasets.

neuroscience↗

bioRxiv2021

Alzheimer's brain inoculation in Aβ-plaque bearing mice: synaptic loss is linked to tau seeding and low microglial activity

Alzheimers disease (AD) is characterized by intracerebral accumulations of extracellular amyloid-{beta} (A{beta}) plaques and intracellular tau pathology that spread in the brain. Tau lesions occur in the form of neuropil threads, neurofibrillary tangles, and neuritic plaques i.e. tau aggregates within neurites surrounding A{beta} deposits. The cascade of events linking these lesions and synaptic or memory impairments are still debated. Intracerebral infusion of human AD brain extracts in A{beta} plaque-bearing mice that do not overexpress pathological tau proteins induces tau pathologies following heterotopic seeding of mouse tau protein. There is however little information regarding the downstream events including synaptic or cognitive repercussions of tau pathology induction in these models. In the current study, human AD brain extracts (ADbe) and control-brain extracts (Ctrlbe) were infused in the hippocampus of A{beta} plaque-bearing APPswe/PS1dE9 mice. Memory, synaptic density, as well as A{beta} plaque and tau aggregate loads, microgliosis, astrogliosis at the inoculation site and in connected regions (perirhinal/entorhinal cortex) were evaluated 4 and 8 months post-inoculation. ADbe inoculation induced memory deficit. It increased deposition of A{beta} plaques close to the inoculation site. Tau pathology was also induced in ADbe-inoculated mice. Neuropil threads and neurofibrillary tangles occurred next to the inoculation site and spread to connected regions notably the perirhinal/entorhinal cortex. Neuritic plaque pathology was detected in both ADbe- and Ctrlbe- inoculated animals but ADbe inoculation increased the severity close and at distance of the inoculation site. Finally, ADbe inoculation reduced synaptic density close to the inoculation site and in connected regions as the perirhinal/entorhinal cortex. Synaptic impairments were correlated with increased severity of neuritic plaques but not of other tau lesions or A{beta} lesions, which suggests that neuritic plaques are a culprit for synaptic loss. Synaptic density was also associated with microglial load. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/438654v4_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@791f29org.highwire.dtl.DTLVardef@1ecf87corg.highwire.dtl.DTLVardef@adb3a0org.highwire.dtl.DTLVardef@1ebef93_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Cancer blues? A validated judgment bias task suggests pessimism in nude mice with tumors

In humans, affective states can bias responses to ambiguous information: a phenomenon termed judgment bias (JB). Judgment biases have great potential for assessing affective states in animals, in both animal welfare and biomedical research. New animal JB tasks require construct validation, but for laboratory mice (Mus musculus), the most common research vertebrate, a valid JB task has proved elusive. Here (Experiment 1), we demonstrate construct validity for a novel mouse JB test: an olfactory Go/Go task in which subjects dig for high- or low-value food rewards. In C57BL/6 and Balb/c mice faced with ambiguous cues, latencies to dig were sensitive to high/low welfare housing, environmentally-enriched animals responding with relative optimism through shorter latencies. Illustrating the versatility of a validated JB task across fields of research, it further allowed us to test hypotheses about the mood-altering effects of cancer (Experiment 2). Male nude mice bearing subcutaneous lung adenocarcinomas responded more pessimistically than healthy controls to ambiguous cues. Similar effects were not seen in females, however. To our knowledge, this is the first validation of a mouse JB task and the first demonstration of pessimism in tumor-bearing animals. This task, especially if refined to improve its sensitivity, thus has great potential for investigating mouse welfare, the links between affective state and disease, depression-like states in animals, and hypotheses regarding the neurobiological mechanisms that underlie affect-mediated biases in judgment.

animal behavior and cognition↗

bioRxiv2020

Zinc potentiates dopamine neurotransmission and cocaine seeking

Cocaine binds to the dopamine (DA) transporter (DAT) to regulate cocaine reward and seeking behavior. Zinc (Zn2+) also binds to the DAT, but the in vivo relevance of this interaction is unknown. We found that Zn2+ concentrations in postmortem brain (caudate) tissue from humans who died of cocaine overdose were significantly lower than in control subjects. Moreover, the level of striatal Zn2+ content in these subjects negatively correlated with plasma levels of benzoylecgonine, a cocaine metabolite indicative of recent use. In mice, repeated cocaine exposure increased synaptic Zn2+ concentrations in the caudate putamen (CPu) and nucleus accumbens (NAc). Cocaine-induced increases in Zn2+ were dependent on the Zn2+ transporter 3 (ZnT3), a neuronal Zn2+ transporter localized to synaptic vesicle membranes, as ZnT3 knockout (KO) mice were insensitive to cocaine-induced increases in striatal Zn2+. ZnT3 KO mice showed significantly lower electrically-evoked DA release and greater DA clearance when exposed to cocaine compared to controls. ZnT3 KO mice also displayed significant reductions in cocaine locomotor sensitization, conditioned place preference (CPP), self-administration, and reinstatement compared to control mice and were insensitive to cocaine-induced increases in striatal DAT binding. Finally, dietary Zn2+ deficiency in mice resulted in decreased striatal Zn2+ content, cocaine locomotor sensitization, CPP, and striatal DAT binding. These results indicate that cocaine increases synaptic Zn2+ release and turnover/metabolism in the striatum, and that synaptically-released Zn2+ potentiates the effects of cocaine on striatal DA neurotransmission and behavior and is required for cocaine-primed reinstatement. In sum, these findings reveal new insights into cocaines pharmacological mechanism of action and suggest that Zn2+ may serve as an environmentally-derived regulator of DA neurotransmission, cocaine pharmacodynamics, and vulnerability to cocaine use disorders.

neuroscience↗

bioRxiv2019

Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility

Impaired lung function is often caused by cigarette smoking, making it challenging to disentangle its role in lung cancer susceptibility. Investigation of the shared genetic basis of these phenotypes in the UK Biobank and International Lung Cancer Consortium (29,266 cases, 56,450 controls) shows that lung cancer is genetically correlated with reduced forced expiratory volume in one second (FEV1: rg=0.098, p=2.3x10-8) and the ratio of FEV1 to forced vital capacity (FEV1/FVC: rg=0.137, p=2.0x10-12). Mendelian randomization analyses demonstrate that reduced FEV1 increases squamous cell carcinoma risk (odds ratio (OR)=1.51, 95% confidence intervals: 1.21-1.88), while reduced FEV1/FVC increases the risk of adenocarcinoma (OR=1.17, 1.01-1.35) and lung cancer in never smokers (OR=1.56, 1.05-2.30). These findings support a causal role of pulmonary impairment in lung cancer etiology. Integrative analyses reveal that pulmonary function instruments, including 73 novel variants, influence lung tissue gene expression and implicate immune-related pathways in mediating the observed effects on lung carcinogenesis.

genetics↗

bioRxiv2018

Chemogenetic ligands for translational neurotheranostics

Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are a popular chemogenetic technology for manipulation of neuronal activity in uninstrumented awake animals with potential for precision medicine-based clinical theranostics. DREADD ligands developed to date are not appropriate for such translational applications. The prototypical DREADD agonist clozapine N-oxide (CNO) lacks brain entry and converts to clozapine. The second-generation DREADD agonist, Compound 21 (C21), was developed to overcome these limitations. We found that C21 has low brain penetrance, weak affinity, and low in vivo DREADD occupancy. To address these drawbacks, we developed two new DREADD agonists, JHU37152 and JHU37160, and the first dedicated positron emission tomography (PET) DREADD radiotracer, [18F]JHU37107. JHU37152 and JHU37160 exhibit high in vivo DREADD potency. [18F]JHU37107 combined with PET allows for DREADD detection in locally-targeted neurons and at their long-range projections, enabling for the first time, noninvasive and longitudinal neuronal projection mapping and potential for neurotheranostic applications.

neuroscience↗

bioRxiv2017

Infants’ neural oscillatory processing of theta-rate speech patterns exceeds adults’

During their early years, infants use the temporal statistics of the speech signal to boot-strap language learning, but the neural mechanisms that facilitate this temporal analysis are poorly understood. In adults, neural oscillatory entrainment to the speech amplitude envelope has been proposed to be a mechanism for multi-time resolution analysis of adult-directed speech, with a focus on Theta (syllable) and low Gamma (phoneme) rates. However, it is not known whether developing infants perform multi-time oscillatory analysis of infant-directed speech with the same temporal focus. Here, we examined infants processing of the temporal structure of sung nursery rhymes, and compared their neural entrainment across multiple timescales with that of well-matched adults (their mothers). Typical infants and their mothers (N=58, median age 8.3 months) viewed videos of sung nursery rhymes while their neural activity at C3 and C4 was concurrently monitored using dual-electroencephalography (dual-EEG). The accuracy of infants and adults neural oscillatory entrainment to speech was compared by calculating their phase-locking values (PLVs) across the EEG-speech frequency spectrum. Infants showed better phase-locking than adults at Theta (~4.5 Hz)and Alpha (~9.3 Hz) rates, corresponding to rhyme and phoneme patterns in our stimuli. Infant entrainment levels matched adults for syllables and prosodic stress patterns (Delta,~1-2 Hz). By contrast, infants were less accurate than adults at tracking slow (~0.5 Hz) phrasal patterns. Therefore, compared to adults, language-learning infants temporal parsing of the speech signal shows highest relative acuity at Theta-Alpha rates. This temporal focus could support the accurate encoding of syllable and rhyme patterns during infants sensitive period for phonetic and phonotactic learning. Therefore, oscillatory entrainment could be one neural mechanism that supports early bootstrapping of language learning from infant-directed speech (such as nursery rhymes).

neuroscience↗

bioRxiv2017

Speaker gaze changes information coupling between infant and adult brains

When infants and adults communicate, they exchange social signals of availability and communicative intention such as eye gaze. Previous research indicates that when communication is successful, close temporal dependencies arise between adult speakers and listeners neural activity. However, it is not known whether similar neural contingencies exist within adult-infant dyads. Here, we used dual-electroencephalography to assess whether direct gaze increases neural coupling between adults and infants during screen-based and live interactions. In Experiment 1 (N=17), infants viewed videos of an adult who was singing nursery rhymes with (a) Direct gaze (looking forward); (b) Indirect gaze (head and eyes averted by 20{degrees}); or (c) Direct-Oblique gaze (head averted but eyes orientated forward). In Experiment 2 (N=19), infants viewed the same adult in a live context, singing with Direct or Indirect gaze. Gaze-related changes in adult-infant neural network connectivity were measured using Partial Directed Coherence. Across both experiments, the adult had a significant (Granger)-causal influence on infants neural activity, which was stronger during Direct and Direct-Oblique gaze relative to Indirect gaze. During live interactions, infants also influenced the adult more during Direct than Indirect gaze. Further, infants vocalised more frequently during live Direct gaze, and individual infants who vocalized longer also elicited stronger synchronisation from the adult. These results demonstrate that direct gaze strengthens bi-directional adult-infant neural connectivity during communication. Thus, ostensive social signals could act to bring brains into mutual temporal alignment, creating a joint-networked state that is structured to facilitate information transfer during early communication and learning.

neuroscience↗