Biology subjects

Lam, J.

Publications and source records attributed to Lam, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Novel Co-expression of Group I Metabotropic Glutamate Receptor During Mouse Cochlear Nucleus Development

Metabotropic glutamate receptors (mGluR) are G-protein coupled receptors that regulate neuroplasticity and have been shown to play a role in auditory processing. However, not much is known about the expression of mGluRs during cochlear nucleus development in the context of Fragile X syndrome (FXS). FXS is the most common heritable form of intellectual disability and autism and is associated with auditory processing deficits including hypersensitivity. Audiogenic seizure is a notable feature of the Fmr1 knock-out (KO) mouse model for FXS, in which mGluR5 has been shown to be necessary. In this study, we investigated the expression of eight metabotropic glutamate receptors (mGluRs) in the cochlear nucleus at both young and adult ages and in wildtype and Fmr1 KO mice. While it is established that mGluR1 is the predominantly expressed mGluR in adult cochlear nucleus, we report the following new finding that mGluR5 is the more abundant receptor during early development. The expression of Group II and III mGluRs (2,3,4,6,7,8) was relatively stable during development. We show that mGluR1 and mGluR5 are co-expressed across multiple neuron types. Fmr1 genotype did not have statistically significant impact on the expression pattern of mGluRs in cochlear nucleus. Although hearing onset occurs during this mGluR5 to 1 transition period, mGluR expression patterns were not impacted by cochlear activity. We conclude that there is an mGluR5 is to mGluR1 transition that occurs within cochlear nucleus neurons during the critical period closure that is intrinsic to neuronal development.

neuroscience↗

bioRxiv2026

HIPPOCAMPAL TAU RELATED SIGNAL INDEXES HYPEREXCITABILITY AND NREM SLEEP MEMORY DYSFUNCTION IN TEMPORAL LOBE EPILEPSY

Background Sleep and memory disturbances are common in temporal lobe epilepsy (TLE), yet their relationship with tau-targeted neuroimaging measures remains unclear. We investigated whether in-vivo temporal 18F-MK6240 tracer retention relates to seizure burden, non-rapid eye movement (NREM) sleep microstructure, and memory performance in TLE. Methods This cross-sectional study was conducted from 2019 to 2024 at the Montreal Neurological Institute-Hospital. Eligible patients had unilateral TLE diagnosed according to International League Against Epilepsy criteria and underwent overnight electroencephalography (EEG) recordings, research-protocol 3T magnetic resonance imaging, and 18F-MK6240 positron emission tomography. Regional 18F-MK6240 standardized uptake value ratios (SUVRs), using the cerebellum as the reference region, were quantified in the ipsilateral hippocampus (defined a priori as the primary region of interest), as well as in peri-hippocampal and lateral temporal regions. Electroclinical and neuropsychological measures, including seizure burden (high vs low), N2 interictal epileptiform discharge frequency (frequent vs non-frequent), and memory performance (impaired vs intact), were classified according to predefined clinical criteria. N2 spindle rate and N3 slow-wave rate were quantified from overnight EEG recordings. Findings Of 70 eligible patients, 25 were included (eight [32%] females; mean age 35.2 years [SD 12.1]). Higher ipsilateral hippocampal 18F-MK6240 uptake was observed in participants with greater focal seizure burden (median [IQR] 0.70 [0.67-0.78] vs 0.64 [0.58-0.65], rank-biserial correlation=-0.58, 95% CI -0.82 to -0.19; p=0.02), was associated with lower N2 spindle rate (r=-0.42, 95% CI -0.70 to -0.03; p=0.04) and higher N3 slow-wave rate (r=0.47; 95% CI 0.09 to 0.73; p=0.02), and was also higher in participants with impaired than intact memory performance (n=21; mean [SD] 0.80 [0.12] vs 0.68 [0.10], Cohen's d=1.15, 95% CI 0.07 to 2.21; p=0.04). Associations outside the hippocampus were generally less consistent and less precise, with the largest non-hippocampal estimate observed in peri-hippocampal regions. Interpretation Higher hippocampal 18F-MK6240 uptake was associated with greater focal seizure burden, altered NREM sleep microstructure, and impaired memory performance in TLE. These findings suggest that hippocampal 18F-MK6240 uptake may represent a candidate marker of circuit vulnerability associated with NREM sleep-memory dysfunction in TLE, warranting validation in larger longitudinal studies.

neuroscience↗

bioRxiv2026

Multiscale alterations and cortex-wide organizational trends in focal cortical dysplasia

BACKGROUND AND OBJECTIVESFocal cortical dysplasia (FCD) is a leading cause of surgically remediable pharmaco-resistant epilepsy. Previous research has used various MRI sequences to profile FCD lesions, but multi-site studies using personalized features derived from sequences routinely used in the clinic are sparse. This study aimed to quantify changes in cortical morphology, myeloarchitecture, and function within FCD lesions, compare MRI signatures between lesion subtypes and outcomes, and investigate links to macroscale brain organization. METHODSThis cross-sectional study included patients with FCD-related epilepsy aggregated across 3 datasets from Canada and Germany. The 3T MRI acquisitions included T1-weighted and fluid-attenuated inversion recovery (FLAIR) sequences, with the addition of a resting-state functional sequence for two datasets. We derived cortex-wide maps of patient-specific variations in morphology, myeloarchitecture, and function. Variations were quantified in lesions, ipsilateral cortex, and homotopic regions using age- and sex-adjusted normative models. Subgroup analyses explored the role of histological subtype and surgical outcome. Variations were also related to anterior-posterior and sensory-association organizational gradients. RESULTSWe included 159 patients with epilepsy and FCD (47 % female) and 183 healthy control participants (50 % female). Lesions exhibited changes in morphology (cortical thickness; FLAIR blurring) and in specific measures of depth-dependent intracortical myelin (variance and kurtosis of intracortical myelin profiles across depths), but not in local function (regional homogeneity; node strength). Spatial contextualization indicated more pronounced thickness changes in transmodal association cortices, while increased blurring of the gray-white matter interface co-localized with posterior cortical regions. FCD Type IIb lesions contained more marked changes in blurring and depth-dependent intracortical myelin (kurtosis of intracortical myelin profiles across depths) than Type IIa lesions. DISCUSSIONOur findings provide robust evidence that multiscale MRI profiling can identify FCD signatures and contribute to in-vivo subtyping. Furthermore, the novel use of myeloarchitecture profiling and contextualization with macro-scale brain gradients provides new avenues to understand intracortical alterations and the embedding of FCD lesions into broader organizational patterns.

neuroscience↗

bioRxiv2026

Pathology in resected areas of FDG PET hypometabolism in pediatric epilepsy patients with focal cortical dysplasia

Introduction[18F]fluorodeoxyglucose positron emission tomography (FDG-PET) frequently reveals hypometabolism extending beyond the epileptogenic zone in focal cortical dysplasia (FCD). However, it is unclear whether these peripheral hypometabolic areas harbour pathological cells potentially contributing to seizure generation. This study characterized histopathology in the lesion epicentre vs borders of the FDG-PET hypometabolism-informed resections in pediatric patients undergoing epilepsy surgery. MethodsFourteen children with intractable, extra-temporal focal epilepsy (mean age 9.0{+/-}5.0 years; 9 female) were retrospectively reviewed. FDG-PET contributed significantly to surgical planning in all cases, with the resection encompassing the visually-apparent MRI signal abnormalities as well as areas of surrounding hypometabolism when safely feasible. Multiple pathological specimens were obtained from the epicentre and surrounding hypometabolic areas. Overall, 136 specimens were analyzed: 64 epicentre (mean 4.6{+/-}3.2/patient) and 72 border (mean 5.1{+/-}3.5/patient). ResultsPathology was identified in 75% of epicentre specimens (59% with frank FCD (fFCD) IIa/b, 16% with dysmorphic neurons only (DNO)). Border specimens showed pathology in 62% (31% fFCD IIa/b, 31% DNO). We fitted a Bayesian logistic mixed model with pathology as outcome variable, location as predictor, and subject as a random effect. Compared to negative pathology, the log-odds of fFCD in the epicentre was 1.00 (confidence interval (CI) 0.32, 1.77) and -1.25 in the border (CI -2.17, -0.40). The log-odds of DNO vs negative pathology was non-significant in both locations. All patients achieved Engel Ia status at one-year follow-up with no long-term neurological deficits. ConclusionThese findings suggest a gradient of histopathology, with fFCD concentrated in the epicentre and DNO present in both the epicentre and hypometabolic borders. Thus, FDG-PET may be used to better detect the histopathological borders of FCD type II, and the high seizure-freedom rate presented here supports the inclusion of these surrounding hypometabolic regions in the surgical resection (when safe to do so), potentially improving the likelihood of removing epileptogenic cells. Key PointsO_LIPathological cells are present not only in the MRI signal abnormality in FCD but also in the periphery of the FDG-PET hypometabolism. C_LIO_LIWe observe a gradient of histopathology, with frank FCD concentrated in the epicentre and dysmorphic neurons spread throughout the area of hypometabolism. C_LIO_LIMaximal safe resection of the area of hypometabolism may increase likelihood of removing epileptogenic cells, thus improving surgical outcome. C_LI

neuroscience↗

bioRxiv2026

MICAFlow: Fast and Robust MRI Preprocessing Bridging Research Neuroimaging and Clinical Practice

MICAFlow is a fully automated MRI preprocessing pipeline designed to translate advanced neuroimaging workflows from research into routine clinical practice. The pipeline emphasizes speed, robustness, and ease of use, focusing on structural and diffusion MRI. Key innovations include a Label-Augmented Modality-Agnostic Registration (LAMAReg) technique driven by deep learning segmentations for reliable cross-modal alignment, integration of state-of-the-art distortion corrections, and adherence to reproducible standards (Snakemake workflow, BIDSApp specifications). We describe the design of MICAFlow and evaluate its performance across heterogeneous datasets. First, accessibility: MICAFlow processes a multimodal MRI exam in minutes with clinically accessible hardware and without requiring GPU access, making it feasible for same-day clinical use. Second, registration accuracy: LAMAReg achieves cutting-edge multi-modal registration accuracy, yielding accurate alignment of diffusion MRI, FLAIR, and intra-subject T1-weighted images while remaining generally robust to common artifacts. Third, data reliability: Using identifiability, we show MICAFlow maintains consistent performance across diverse datasets, including subjects with pathology, and is closely comparable to contemporary pipelines. In sum, MICAFlows combination of machine learning and efficient workflows produces research-grade data quality with clinical-grade speed. This work demonstrates that advanced MRI preprocessing can be done fast and robustly, helping close the gap between research neuroimaging and broad clinical application of quantitative MRI techniques. The source code for MICAFlow is available here: https://github.com/MICA-MNI/micaflow, and for LAMAReg here: https://github.com/MICA-MNI/LAMAReg.

bioinformatics↗

bioRxiv2026

Precision mapping and molecular contextualization of surgical outcome epicenters in temporal lobe epilepsy

AO_SCPLOWBSTRACTC_SCPLOWTemporal lobe epilepsy is the most common drug-resistant epilepsy, with surgical resection offering the primary path to seizure freedom. Despite standardized approaches, a substantial proportion of patients experience seizure recurrence, and the neurobiological substrates underlying these divergent outcomes remain unclear. We applied an individualized normative modeling framework to multimodal preoperative MRI data in a group that subsequently underwent surgical resection, to characterize patient-specific structural deviations and identify disease epicenters. Patients who became seizure-free exhibited spatially coherent abnormalities localized to the hippocampus and ipsilateral association regions, anchored in agranular limbic territories and enriched for genes linked to calcium-dependent signaling. Non-seizure-free patients, on the other hand, showed a more heterogeneous and distributed pattern of deviations, consistent with a "temporal-plus" network organization, and broader neuromodulatory dysregulation. Crucially, overlap between resected tissue and network-defined epicenters was closely associated with seizure freedom, independent of total resection volume. These findings provide a multiscale framework for precision surgical planning, shifting the focus from standardized tissue removal to targeted disconnection of patient-specific pathological hubs.

neuroscience↗

bioRxiv2025

An open dataset of cerebral tau deposition in young healthy adults based on MK6240 positron emission tomography

Tauopathies are pathologies wherein phosphorylated insoluble tau aggregates in neurons, leading to dysfunction and degeneration. Positron emission tomography (PET) enables measurement of in vivo tau, with second-generation radiotracers such as [18F]MK6240 showing high tau affinity with minimal off-target binding. While tauopathies are commonly linked to age-related neurodegenerative diseases, notably Alzheimers disease (AD), evidence suggests pathophysiological cascades may begin long before clinical onset. Increasingly, tau is recognized in pathologies affecting younger individuals, including autosomal dominant AD, Niemann-Pick disease type C, chronic traumatic encephalopathy, and epilepsy, thus highlighting the importance of normative data in non-geriatric populations. Here, we present a dataset of 33 young to middle-age healthy adults (mean age 34.0{+/-}10.4 years, 12 female) with [18F]MK6240 PET data and T1w magnetic resonance imaging. Longitudinal data are also available in a subset of 9 participants with a minimum follow-up time of 1 year. Our dataset aims to support imaging biomarker studies on younger individuals potentially at risk for AD and to advance work in tauopathies affecting non-geriatric populations generally excluded from neurodegeneration studies.

neuroscience↗

bioRxiv2025

VesicleVoyager: In vivo selection of surface displayed proteins that direct extracellular vesicles to tissue-specific targets

The development of technologies for screening proteins that bind to specific tissues in vivo and facilitate delivery of large cargos remains challenging, with most approaches limited to cell culture systems that often yield clinically irrelevant hits. To overcome this limitation, we developed a novel molecular screening platform using an extracellular vesicle (EV) display library. EVs are natural molecular carriers capable of delivering diverse cargos, which can be engineered to enhance specificity and targeting through surface modifications. We constructed an EV-display library presenting monobody repertoires on EV surfaces, with genetic cargo inside the EVs corresponding to the displayed proteins. These libraries were screened for tissue specific delivery through serial passage in mice via sequential intravenous administration in and recovery of tissue-selected EVs and amplification of their encapsulated monobody genes at each passage. Our results demonstrated successful selection of tissue-specific targeting proteins, as revealed by fluorescence and bioluminescence imaging followed by DNA sequencing. To understand the stochastic relationship between displayed proteins and packaged genes, we developed a Markov chain model that quantified selection dynamics and predicted enrichment patterns despite the imperfect correlation between phenotype and genotype. This EV-based monobody screening approach, combined with mathematical modeling, is a significant advancement in targeted drug delivery by leveraging the natural capabilities of EVs with the selection of targeting proteins in a physiologically relevant environment.

bioengineering↗

bioRxiv2025

In-vivo evidence for increased tau deposition in temporal lobe epilepsy

Temporal lobe epilepsy (TLE), the most common pharmaco-resistant epilepsy in adults, has been linked to structural brain changes extending beyond the mesiotemporal areas. While not traditionally viewed as a neurodegenerative disorder, recent ex-vivo studies have shown elevated levels of misfolded tau protein in TLE. This study investigated tau deposition in TLE patients using the in-vivo PET tracer [18F]MK-6240. We studied 28 TLE patients and 28 healthy controls to assess tau uptake and its relationship with brain connectivity, clinical variables, and cognitive function alongside post-surgical tissue from a subset of patients. Compared to controls, TLE patients exhibited markedly increased [18F]MK-6240 uptake in bilateral superior and medial temporal regions and the parietal cortex, with tau accumulation following regional functional and structural connectivity and cognitive impairment. Immunohistochemistry analysis confirmed variable phosphorylated tau staining in 5/6 operated cases with available specimens. These findings suggest that tau accumulation contributes to cognitive decline observed in TLE, supporting a potential role of tau in epilepsy-related neurodegeneration.

neuroscience↗

bioRxiv2025

In-House Manufacturing of 3D Culture Chips via Vacuum Thermoforming for Enhanced Imaging Applications

Engineered 3D in vitro cancer models, particularly those that facilitate image-based readouts capable of distinguishing the behavior of different cell populations, have become crucial tools in the discovery process. One such model, 96-GLAnCE (Gels for Live Analysis of Compartmentalized Environments), allows for longitudinal imaging of tumor cell dynamics and therapy response. However, the widespread adoption of 96-GLAnCE has been limited by the need for expensive, specialized fabrication equipment. To overcome this challenge, we have optimized a desktop vacuum thermoforming technique for the in-house production of 96- GLAnCE bottom chips using thin polystyrene films. This optimization has led to the reliable and consistent fabrication of devices. Notably, using thin polystyrene films reduces the overall thickness of the chips, enabling high-magnification imaging for studying primary tumor cell phenotypes in 3D with single-cell and subcellular resolution. Our thermoformed devices offer a flexible, cost-effective solution for addressing a wide range of biological questions across various time scales.

bioengineering↗

bioRxiv2025

Network-based population analysis of 31,595 gonococcal genomes reveals phase variability, genetic diversity and mobile element dynamics drive antimicrobial resistance and phenotypic diversity

With a highly plastic genome allowing the accumulation of antimicrobial resistance (AMR) determinants, Neisseria gonorrhoeae (Ngo) is an urgent public health threat. To better understand the spread of AMR in Ngo and its ability to persist in humans, we performed a systematic analysis of its global population structure. From 31,595 publicly available genomes, we curated a maximally diverse representative set of 485 gonococcal genomes, which were defined into 12 distinct clades on the basis of shared patterns of single nucleotide polymorphisms. Mapping AMR determinants and mobile elements onto these clades revealed significant correlation with gonococcal population structure. Notably, several variants associated with AMR were identified in genes not previously linked with resistance, suggesting roles as new determinants of resistance or compensatory mutations in resistant strains. Analysis of phase variable motifs, a significant mechanism driving regulation of expression in Ngo, identified 57 genes not previously identified as phase variable; in vivo and in vitro passaging validated our sequence-based definition of phase variability and revealed a strong association of phase variation of the surface proteins Opa and LgtG with improved colonization during infection. Together these findings highlight the ability of systematic comparative genomic analyses to shed new light on the drivers of Ngo population structure and identify new AMR determinants.

microbiology↗

bioRxiv2024

Structural compromise in spiking cortex and connected networks

INTRODUCTIONEpilepsy is increasingly conceptualized as a network disorder, and advancing methods for its diagnosis and treatment requires characterizing both the epileptic generator and related networks. We combined multimodal magnetic resonance imaging (MRI) and high-density electroencephalography (HD-EEG) to interrogate alterations in cortical microstructure, morphology, and intrinsic local function within and beyond spiking tissue in focal epilepsy. METHODSWe studied 25 patients with focal epilepsy (12F, mean {+/-} SD age = 31.28 {+/-} 9.30 years) and 55 age- and sex-matched healthy controls, subdivided into a group of 30 for imaging feature normalization (15F, 31.40 {+/-} 8.74 years) and a group of 25 for replication (12F, 31.04 {+/-} 5.65 years). The 3T MRI acquisition included T1-weighted, diffusion, quantitative T1 relaxometry, and resting-state functional imaging. Open-access MRI processing tools derived cortex-wide maps of morphology and microstructure (cortical thickness, mean diffusivity, and quantitative T1 relaxometry) and intrinsic local function and connectivity (timescales, connectivity distance, and node strength) for all participants. Multivariate approaches generated structural and functional alteration scores for each cortical location. Using HD-EEG electrical source imaging, the most prominent spike type was localized and we quantified MRI alterations within spike sources, as well as in proximal and connected networks. RESULTSRegions harboring spike sources showed increased structural MRI alterations compared to the rest of the brain in patients. Structural compromise extended to all regions with close functional coupling to spike sources, but not to anatomical neighbors of spike sources. This finding was replicated using average control functional and anatomical matrices instead of patient-specific matrices. CONCLUSIONSpiking regions contain more marked alterations in microstructure and morphology than the remaining cortex, and combining imaging with neurophysiology techniques may ultimately help identify the epileptogenic zone non-invasively. There are nevertheless broader networks effects, which may relate to a cascading of structural changes to functionally connected cortices. These results underscore the utility of combining high-definition MRI and EEG approaches for characterizing epileptogenic tissue and assessing distributed network effects.

neuroscience↗

bioRxiv2024

Adjuvant-dependent impacts on vaccine-induced humoral responses and protection in preclinical models of nasal and genital colonization by pathogenic Neisseria

Neisseria gonorrhoeae, which causes the sexually transmitted infection gonorrhea and N. meningitidis, a leading cause of bacterial meningitis and septicemia, are closely related human-restricted pathogens that inhabit distinct primary mucosal niches. While successful vaccines against invasive meningococcal disease have been available for decades, the rapid rise in antibiotic resistance has led to an urgent need to develop an effective gonococcal vaccine. Several surface antigens are shared among these two pathogens, making cross-species protection an exciting prospect. However, the type of vaccine-mediated immune response required to achieve protection against respiratory versus genital infection remains ill defined. In this study, we utilize well established mouse models of female lower genital tract colonization by N. gonorrhoeae and upper respiratory tract colonization by N. meningitidis to examine the performance of transferrin binding protein B (TbpB) vaccines formulated with immunologically distinct vaccine adjuvants. We demonstrate that vaccine-mediated protection is influenced by the choice of adjuvant, with Th1/2-balanced adjuvants performing optimally against N. gonorrhoeae, and both Th1/2-balanced and Th2-skewing adjuvants leading to a significant reduction in N. meningitidis burden. We further establish a lack of correlation between protection status and the humoral response or bactericidal titre. Combined, this work provides supports the feasibility for a single vaccine formulation to achieve pan-neisserial coverage.

immunology↗

bioRxiv2024

Rational selection of TbpB variants elucidates a bivalent vaccine formulation with broad spectrum coverage against Neisseria gonorrhoeae

Neisseria gonorrhoeae is the causative agent of gonorrhea, an on-going public health problem due in part to the lack of success with efforts to develop an efficacious vaccine to prevent this sexually transmitted infection. An attractive candidate vaccine antigen because of its essential function and surface exposure, the gonococcal transferrin binding protein B (TbpB) exhibits high levels of antigenic variability which poses a significant obstacle in evoking a broadly protective vaccine composition. Here, we utilize phylogenetic information to rationally select TbpB variants for inclusion into a potential gonococcal vaccine and identify two TbpB variants that when formulated together elicit a highly cross-reactive antibody response in both rabbits and mice against a diverse panel of TbpB variants and clinically relevant gonococcal strains. Further, this formulation performed well in experimental proxies of real-world usage, including eliciting bactericidal activity against 8 diverse gonococcal strains and decreasing the median duration of colonization after vaginal infection in female mice by two heterologous strains of N. gonorrhoeae. Together, these data support the use of a combination of TbpB variants for a broadly protective gonococcal vaccine.

microbiology↗

bioRxiv2024

Analyzing high-throughput assay data to advance the rapid screening of environmental chemicals for human reproductive toxicity

While high-throughput (HTP) assays have been proposed as platforms to rapidly assess reproductive toxicity, there is currently a lack of established assays that specifically address germline development/function and fertility. We assessed the applicability domains of yeast (S. cerevisiae) and nematode (C. elegans) HTP assays in toxicity screening of 124 environmental chemicals, determining their agreement in identifying toxicants and their concordance with reproductive toxicity in vivo. We integrated data generated in the two models and compared results using a streamlined, semi-automated benchmark dose (BMD) modeling approach. We then extracted and modeled relevant mammalian in vivo data available for the matching chemicals included in the Toxicological Reference Database (ToxRefDB). We ranked potencies of common compounds using the BMD and evaluated correlation between the datasets using Pearson and Spearman correlation coefficients. We found moderate to good correlation across the three data sets, with r = 0.48 (95% CI: 0.28-1.00, p<0.001) and rs = 0.40 (p=0.002) for the parametric and rank order correlations between the HTP BMDs; r = 0.95 (95% CI: 0.76-1.00, p=0.0005) and rs = 0.89 (p=0.006) between the yeast assay and ToxRefDB BMDs; and r = 0.81 (95% CI: 0.28-1.00, p=0.014) and rs = 0.75 (p=0.033) between the worm assay and ToxRefDB BMDs. Our findings underscore the potential of these HTP assays to identify environmental chemicals that exhibit reproductive toxicity. Integrating these HTP datasets into mammalian in vivo prediction models using machine learning methods could further enhance the predictive value of these assays in future rapid screening efforts.

developmental biology↗

bioRxiv2024

Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity

Reproduction is a functional outcome that relies on complex cellular, tissue, and organ interactions that span the developmental period to adulthood. Thus, the assessment of its disruption by environmental chemicals is remarkably painstaking in conventional toxicological animal models and does not scale up to the number of chemicals present in our environment and requiring testing. We adapted a previously described low-throughput in vivo chromosome segregation assay using C. elegans predictive of reproductive toxicity and leveraged available public data sources (ToxCast, ICE) to screen and characterize 133 physiologically-relevant chemicals in a high-throughput manner. The screening outcome was further validated in a second, independent in vivo assay assessing embryonic viability. In total, 13 chemicals were classified as reproductive toxicants with the two most active chemicals belonging to the large family of Quaternary Ammonium Compounds (QACs) commonly used as disinfectants but with limited available reproductive toxicity data. We compared the results from the C. elegans assay with ToxCast in vitro data compiled from 700+ cell response assays and 300+ signaling pathways-based assays. We did not observe a difference in the bioactivity or in average potency (AC50) between the top and bottom chemicals. However, the intended target categories were significantly different between the classified chemicals with, in particular, an over-representation of steroid hormone targets for the high Z-score chemicals. Taken together, these results point to the value of in vivo models that scale to high-throughput level for reproductive toxicity assessment and to the need to prioritize the assessment of QACs impacts on reproduction.

pharmacology and toxicology↗

bioRxiv2023

Genome folding principles revealed in condensin-depleted mitotic chromosomes

During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co- depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1, HP1{Pi} and HP1{gamma}, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensin-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.

genomics↗

bioRxiv2023

G6PD Maintains Redox Homeostasis and Biosynthesis in LKB1-Deficient KRAS-Driven Lung Cancer

Cancer cells depend on nicotinamide adenine dinucleotide phosphate (NADPH) to combat oxidative stress and support reductive biosynthesis. One major NAPDH production route is the oxidative pentose phosphate pathway (committed step: glucose-6-phosphate dehydrogenase, G6PD). Alternatives exist and can compensate in some tumors. Here, using genetically-engineered lung cancer model, we show that ablation of G6PD significantly suppresses KrasG12D/+;Lkb1-/-(KL) but not KrasG12D/+;p53-/- (KP) lung tumorigenesis. In vivo isotope tracing and metabolomics revealed that G6PD ablation significantly impaired NADPH generation, redox balance and de novo lipogenesis in KL but not KP lung tumors. Mechanistically, in KL tumors, G6PD ablation caused p53 activation that suppressed tumor growth. As tumor progressed, G6PD-deficient KL tumors increased an alternative NADPH source, serine-driven one carbon metabolism, rendering associated tumor-derived cell lines sensitive to serine/glycine depletion. Thus, oncogenic driver mutations determine lung cancer dependence on G6PD, whose targeting is a potential therapeutic strategy for tumors harboring KRAS and LKB1 co-mutations.

cancer biology↗