Biology subjects

Thompson, C.

Publications and source records attributed to Thompson, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Shaping cryogenic 3D volume imaging by pFIB ion species and milling voltage

Cryogenic plasma focused ion beam-scanning electron microscopy (cryo-pFIB-SEM) enables nanoscale volume imaging of vitrified cells and tissues, but the fidelity of each newly exposed block-face depends on how ions interact with compositionally heterogeneous biological material. Using xenon, argon, oxygen, and nitrogen plasma beams across a 30-2 kV voltage range, we examined how ion species and accelerating voltage influence block-face quality and ultrastructural fidelity. Curtaining imposed a species-dependent lower limit on accelerating voltage, with xenon and argon supporting uniform milling to 10 kV and oxygen and nitrogen to 15 kV. Monte Carlo simulations predicted substantially reduced ion penetration and atomic displacement under these species-specific low-kV conditions. Experimentally, lowering milling voltage suppressed charging and topographic artifacts, with the largest effects observed at heterogeneous interfaces. Oxygen and nitrogen produced greater membrane sharpness and organelle contrast than the noble gases, and these differences influenced machine-learning-based recognition of fine organelle features in 3D datasets. Together, these findings show that cryo-pFIB-SEM image quality cannot be optimized by accelerating voltage or ion species independently. Instead, milling performance reflects a tradeoff among surface fidelity, charging, contrast, and curtaining that depends on local specimen composition. Species-specific low-kV milling therefore provides a practical framework for matching cryo-pFIB-SEM acquisition conditions to the structural and biophysical properties of the biological target.

cell biology↗

bioRxiv2026

Depth-resolved analysis reveals target-dependent cryo-FIB damage profiles

Cryogenic focused ion beam (cryo-FIB) milling enables cellular cryo-electron tomography but can compromise high-resolution structural information near milled surfaces. Here we establish recombinant human apoferritin (apoF) as a reporter of depth-dependent structural preservation in cellular lamellae. ApoF yielded a 2.05 [A] in situ reconstruction. Apparent FIB damage was most pronounced within the first 15 nm for xenon, 30 nm for gallium, 45 nm for argon and remained detectable at least 75 nm from oxygen-milled surfaces under the workflows tested. Endogenous 70S ribosomes in the same xenon-milled tomograms showed a broader 30-45 nm profile, whereas {beta}-galactosidase showed a similar narrow xenon-associated profile in a different specimen. Xenon-milled lamellae 125-150 nm thick yielded the highest resolution among the thickness groups examined, with lower resolution in the thinner and thickest groups. These findings show structural preservation is constrained by both surface-associated damage and lamella thickness, with the apparent extent of damage varying by molecular reporter. Previous ribosome-based surface-exclusion estimates may therefore be overly conservative for some molecular targets.

molecular biology↗

bioRxiv2026

MTERF1 loss buffers against pathogenic mtDNA deletions through transcriptional regulation

Large-scale mitochondrial DNA (mtDNA) deletions cripple oxidative phosphorylation once they exceed a critical heteroplasmy threshold, causing incurable mitochondrial pathologies. Using a genome-wide CRISPR/Cas9 screen in an engineered human cell line carrying a large-scale mtDNA deletion at high heteroplasmy, we identified mitochondrial transcription termination factor 1 (MTERF1) as a suppressor of the heteroplasmy burden. Loss of MTERF1 restored mitochondrial function and increased cellular proliferation in cells with a mtDNA deletion burden exceeding the pathogenic threshold, without altering heteroplasmy or mtDNA copy number. MTERF1 binds wild-type and deletion-bearing mitochondrial genomes indiscriminately at a site downstream of the ribosomal RNA genes and curbs transcription. Relieving this constraint broadly increased OXPHOS transcripts, thereby eliciting more respiratory output from the residual wild-type genomes. Notably, the buffering effect of MTERF1 loss extended beyond mtDNA deletions. In a counter-screen, MTERF1 loss could also restore respiratory growth in cells depleted of nuclear-encoded mitochondrial genes such as OPA1 and COX5A. Together, these findings indicate that by relieving a transcriptional constraint, MTERF1 loss compensates for reduced genome dosage, defining a strategy to enhance residual mitochondrial function in mtDNA deletion disorders and related conditions.

molecular biology↗

bioRxiv2026

Evaluating the potential role and contribution of transposable elements to the evolution of microbial multicellularity across the tree of eukaryotes

Multicellularity has evolved multiple times across the eukaryotic tree of life, including among protist lineages. Because transposable elements (TEs) strongly influence genome architecture and gene regulation, understanding their potential impact on genome structure and their relationship with gene expression may provide insight into the evolution of multicellularity. Here, we generated a new genome assembly for the facultatively multicellular amoeba Acrasis kona and performed comparative analyses of TE composition, TE diversity, and TE-density organization across diverse protist lineages. Comparative analyses included unicellular and multicellular representatives from across the tree of eukaryotes, (Heterolobosea, Filasterea, Cristidiscoidea, and Chlorophyceae), including Naegleria spp., Tetramitus jugosus, Capsaspora owczarzaki, Pigoraptor spp., Fonticula alba, Parvularia atlantis, Volvox carteri, and Chlamydomonas reinhardtii. To examine relationships between TEs and gene regulation, we integrated transcriptomic datasets from A. kona, Capsaspora owczarzaki, and Volvox carteri with genome-wide TE-density analyses of differentially expressed genes. TE abundance and composition varied substantially among lineages, with species that exhibit more complex developmental or cellular organization generally containing higher TE proportions than closely related unicellular taxa. Patterns of TE-density organization near up-regulated, down-regulated, and non-differentially expressed genes also differed among systems, ranging from strong TE depletion in A. kona to weaker or cell-type-specific patterns in Capsaspora and Volvox. Together, these findings suggest that transposable elements are associated with multicellularity across diverse protist lineages, although the specific roles they play appear to be complex, lineage-specific, and not yet fully understood.

genetics↗

bioRxiv2026

A Community Standard Multispecies Cell Atlas of the Basal Ganglia

The NIH BRAIN Initiative Cell Atlas Network (BICAN) aims to generate a standardized, integrated cell atlas of the human, macaque, marmoset, and mouse brain that serves as a foundational community reference for the classification and study of brain cell types. Here we present the first major component of this effort: a cross-species, multimodal atlas of the basal ganglia, a group of subcortical nuclei central to motor control and implicated in a broad range of neurological disorders. Grounded in large-scale single-cell transcriptomic classification and integrated with epigenomic and spatial genomic modalities, this resource is enabled by coordinated cross-species sampling and harmonized analytical frameworks. It provides extensive phenotypic characterization of cell types, incorporates community-informed annotation, and establishes a highly curated, data-driven taxonomy with standardized nomenclature. The atlas is anchored to species-specific anatomical reference frameworks and linked across species through unified structural ontologies, enabling consistent cross-species comparisons. Multiple complementary datasets are mapped to this reference, including multiomic profiles and developmental trajectories aligned to adult cell states. Realization of this resource has required coordinated standards for tissue processing across human and model organisms, harmonization of donor metadata across brain banks, and the development of unified anatomical reference systems. To support these advances, BICAN has established an integrated ecosystem comprising standardized sequencing pipelines, neuroanatomically grounded data infrastructure, scalable visualization and mapping tools, and interoperable metadata standards. Analogous to the standardization achieved in genome science, this ecosystem provides a FAIR (findable, accessible, interoperable, and reusable) framework that enables researchers to map, compare, and interpret diverse datasets against a shared reference and associated knowledge base. The BICAN reference system is now being extended to the whole brain, with principles that are readily generalizable to other organ systems.

neuroscience↗

bioRxiv2026

Temporal AI model predicts drivers of cell state trajectories across human aging

Foundational AI models have recently shown promise for predicting the impact of perturbations on cell states. However, current models typically consider only one cell state at a time, limiting their ability to learn how cellular responses unfold over time, particularly across long trajectories such as diseases of aging. Here, we develop a temporal AI model, MaxToki, trained on nearly 1 trillion gene tokens including cell state trajectories across the human lifespan to generate cell states across long timelapses of human aging. MaxToki generalized to unseen trajectories through in-context learning and predicted novel age-modulating targets that were experimentally verified to influence age-related gene programs and functional decline in vivo. MaxToki represents a promising strategy for temporal modeling to accelerate the discovery of interventions for programming therapeutic cellular trajectories.

bioinformatics↗

bioRxiv2026

A systematic analysis of brain tissue response to microelectrode material and size with single-cell spatial transcriptomics

Implantable microelectrode arrays can interface with the central nervous system to record from and/or stimulate neural tissues to treat neurological disease and injury. The chronic tissue response to implanted electrodes is believed to be a driving factor behind microelectrode failure. Next-generation electrodes have been developed to attenuate the tissue response by reducing electrode size and/or incorporating softer materials. In this study, we used single-cell-resolution spatial transcriptomics to quantify the tissue response to implanted electrodes within custom-classified cell types in the rat brain. To test the effects of implant material and size, we assessed polyimide and silicon electrodes of 10 {micro}m and 100 {micro}m cross-sectional dimensions over 6-weeks post-implantation. Our data indicate that implants are associated with upregulation of inflammatory genes in glia that are coupled to damage-initiated losses in synaptic transmission and subsequent engagement of compensatory protective mechanisms (e.g., re-myelination, antioxidant production) to preserve local neurons. While bulk tissue analysis reinforced previously reported observations of glial scar consolidation over time, single cell analysis revealed an unexpected, progressive heightening of the expression of inflammatory genes in individual device-reactive astrocytes. With respect to design features, the impact of device dimensions more heavily influenced responses than material type, particularly by the 6-week time point. Our results add single-cell resolution observations to the growing use of transcriptomics to understand the biocompatibility of devices implanted in the brain.

neuroscience↗

bioRxiv2026

Integrating Lateral Super-resolution and Axial Progression Reveals Distinct Clathrin Pit Formation Pathways

Clathrin-mediated endocytosis (CME) relies on the dynamic assembly and remodeling of clathrin coats to drive membrane curvature and vesicle formation at the plasma membrane. Although live-cell fluorescence microscopy has provided critical insights into the timing and molecular composition of endocytic events, directly linking the nanoscale lateral organization of clathrin coats to their three-dimensional progression in real time has remained challenging. Structural approaches such as electron microscopy provide detailed snapshots of clathrin architecture but are inherently static, whereas axial TIRF-based methods report membrane-proximal position with limited lateral resolution. Here, we introduce variable-angle total internal reflection fluorescence structured illumination microscopy (vaTIRF-SIM), a live-cell imaging strategy that integrates lateral super-resolution with dynamic axial sensitivity near the plasma membrane. By combining TIRF-SIM with controlled variation of the evanescent field penetration depth, vaTIRF-SIM enables simultaneous visualization of clathrin coat architecture and relative axial displacement with high spatial and temporal resolution. Applying this approach to de novo clathrin-coated pits reveals coordinated lateral growth and progressive axial advancement from early stages of pit formation through maturation, consistent with early curvature generation that intensifies over time. Extending this analysis to clathrin plaques uncovers two distinct plaque-associated endocytic behaviors: slowly maturing pits that originate at plaque peripheries and progress similarly to de novo pits, and rapid plaque subdomain internalization events marked by accelerated axial progression. Together, these results establish vaTIRF-SIM as an approach that, for the first time, enables direct real-time coupling of nanoscale clathrin coat organization with axial progression during CME in living cells.

biophysics↗

bioRxiv2026

Zwitterionic polymer coating enabled chronic dopamine sensing and electrophysiology recording in free-moving mice

The brains complex network relies on both electrical and chemical signaling to support its physiological and cognitive functions. To fully understand neural circuit dynamics and their dysfunctions, it is crucial to simultaneously detect neurotransmitters and modulators alongside electrophysiological signals. The striatal dopamine circuits are integral to neurological processes such as movement, reward, learning, and circadian rhythm regulation, making it highly desirable to monitor both neural activity and dopamine (DA) levels in freely behaving animals. One promising approach involves the implantation of multimodal microelectrode arrays (MEAs). However, chronic electrochemical sensing of DA in freely moving animals faces significant challenges, including biofouling of sensing electrodes and the instability of Ag/AgCl reference electrodes. In this study, we developed two complementary strategies--surface grafting and photo crosslinking--to coat the MEA and implanted Ag/AgCl reference electrodes, respectively, with zwitterionic poly(sulfobetaine methacrylate) (PSB). The surface-grafted thin PSB coating effectively inhibits protein fouling and inflammatory responses to the MEA, while the PSB hydrogel protects the Ag/AgCl electrodes from delamination in vivo, ensuring a stable reference potential. By coating both the Ag/AgCl reference electrodes and flexible polyimide MEAs with PSB and PEDOT/CNT, we achieved stable DA detection and electrophysiological recordings in freely moving mice over a four-week period. Weekly electrochemical impedance spectroscopy confirmed the long-term stability of the implanted electrodes. Our method enables multidimensional analysis of behavioral patterns, electrophysiological activity, and DA dynamics, providing a comprehensive approach for neuroscience research. This work advances neurochemical and electrophysiological methodologies by offering reliable tools for longitudinal investigations of brain function in freely behaving animals.

bioengineering↗

bioRxiv2026

Dual Role of Ninjurin-1 in Myeloid Cell Adhesion and Inflammation in Relapse-Remitting EAE

Nerve Injury-Induced Protein 1 (Ninjurin-1) is an adhesion molecule implicated in inflammation and tissue injury, yet its role in neuroinflammatory diseases such as multiple sclerosis (MS) remains poorly defined. Here, we identify Ninjurin-1 as a key mediator of immune activation and CNS infiltration in relapsing-remitting experimental autoimmune encephalomyelitis (RR-EAE), a model of relapsing-remitting MS (RRMS). Using flow cytometry, gene-expression profiling, and in vivo peptide blockade, we show that Ninjurin-1 is markedly upregulated on CNS-infiltrating myeloid cells during disease progression. Ninjurin-1 myeloid cells display a dual function, as both an adhesion molecule and a marker of inflammatory activation, characterized by increased antigen presentation, cytokine production, and transcriptional enrichment for genes regulating adhesion, migration, and innate immune signaling. Importantly, therapeutic blockade of Ninjurin-1 significantly reduced clinical severity, CNS immune infiltration, and demyelination in RR-EAE. These findings uncover a previously unrecognized role for Ninjurin-1 in myeloid-driven neuroinflammation and highlight its potential as a therapeutic target for relapsing-remitting MS.

neuroscience↗

bioRxiv2025

The evolution of public goods altruism

Organisms often behave altruistically by investing resources into public goods production. Because the rewards of public goods are freely available to everyone in a group, they are potentially vulnerable to exploitation by cheaters. Classic kin selection models offer solutions to this public goods dilemma in terms of why public goods investment can be favoured, while game theoretical models offer insights into the conditions where exploitative cheaters can persist. However, existing theory does not provide a unified framework for understanding how much individuals should actually invest in altruism or how this investment strategy relates to why cheaters can coexist with altruists. Here we fill this gap by considering how resource allocation trade-offs shape the generosity of altruists, how this investment decision, in turn, sets the conditions for cheater coexistence, and how local competition impacts these outcomes. We find that, whenever altruists can evolve the optimal level of public goods investment, they exclude cheaters, revealing that stable altruists/cheater coexistence requires overly generous altruists--an outcome frequently driven by mechanistic constraints that limit the range of behaviours in biological systems. Importantly, we show that local competition tends to prevent such coexistence. By capturing key biologically relevant factors, our model provides a compelling framework for interpreting patterns of variation in altruistic behaviour in natural populations, and a means of generating testable predictions.

evolutionary biology↗

bioRxiv2025

Serological evidence of SARS-CoV-2 infection in red and fallow deer in Great Britain.

SARS-CoV-2 is the viral agent of COVID-19 disease in humans and has been shown to infect a wide range of mammals, including white-tailed deer in North America and fallow deer in the Republic of Ireland. There are six species of deer in the UK which inhabit both urban and rural areas, providing a broad interface for human-deer interaction. Little is known if British deer species act as a reservoir for zoonotic spread of consequence to human health. Here, we report a high seroprevalence of SARS-CoV-2 neutralising antibodies in British deer, adding native red deer to the list of susceptible species. 62% of fallow and 25% of red deer sampled between 2024 and 2025 from one British deer park were positive for SARS-CoV-2 infection by serology. Data suggest that deer may function as permissive, reservoir-capable hosts and highlight the risks of anthroponosis and zoonosis from unregulated human-deer contact. While there is currently no evidence to suggest that these viruses are persisting within deer populations in Great Britain, the animal origins of SARS-CoV-2 highlight the importance of appropriate and limited interactions with wildlife, to minimise transmission risks and safeguard both animal and human health.

microbiology↗

bioRxiv2025

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens

We present a platform that directly sequences single guide RNAs and endogenous 3'UTRs in fixed cells while simultaneously measuring protein abundance and cellular morphology. We demonstrate platform capability by performing optical pooled screening of CRISPR-perturbed lung cancer cells. This approach unites direct in-sample RNA sequencing with complementary phenotypic readouts, enabling comprehensive, scalable, and functional genomics analyses within a single experiment.

genomics↗

bioRxiv2025

Korean Natural Farming practices are dominated by a limited number of microbes and decrease fungal diversity

Korean Natural Farming (KNF) practices claim to cultivate and transfer "indigenous micro-organisms" (IMOs) to donor soils as a method of probiotic soil enhancement. We investigated whether IMO cultivation can propagate unique microbiomes and maintain microbial diversity through successive IMO stages for restoration of flood contaminated soils. Employing a balanced study design using soil samples from salt marsh, deciduous forest, and urban greenspace (plus sterilized controls), samples underwent the first two IMO cultivation steps followed by 16S rRNA and ITS metagenomic sequencing. Notably, IMO cultivation was dominated by limited bacterial taxa (Enterobacterales, Pseudomonadales, Bacillales) and fungal taxa (Rhizopodaceae, particularly R. oryzae). While bacterial diversity was maintained or increased during two IMO stages, fungal diversity consistently decreased. Principal Coordinates Analysis also revealed distinct clustering by inoculum source (i.e. human-altered, human- transported (HAHT) vs. natural vs. sterile) that persisted throughout cultivation. Our evidence suggests that the IMO process enriches for specific taxa likely adapted to cultivated conditions and fails to maintain fungal diversity, contrasting greatly with KNFs proposed benefit of propagating locale-specific, fungal-dominated indigenous microbiomes. However, our results demonstrate that early IMO cultures may capture and sustain bacterial diversity in soil, opening the door for future studies of KNF efficacy and sustainability. Sustainability StatementThis work is primarily associated with UN Sustainable Development Goal SDG 15 (Life on Land). By scientifically evaluating Korean Natural Farming "indigenous Microorganism" (IMO) practices through metagenomic sequencing, this study provides evidence-based insights into microbial community dynamics relevant to soil restoration and terrestrial ecosystem health. The findings inform low-cost bioremediation strategies for flood- contaminated urban soils, which is of growing importance as climate-driven extreme precipitation events intensify. Additional relevant SDGs include: SDG 13 (Climate Action), SDG 11 (Sustainable Cities and Communities), SDG 2 (Zero Hunger), and SDG 3 (Good Health and Well-being).

microbiology↗

bioRxiv2025

Initiation of human cytomegalovirus secondary envelopment requires the gM/gN glycoprotein complex and involves palmitoylation.

Glycoprotein M (gM) of human cytomegalovirus (HCMV) forms a protein complex with glycoprotein N (gN), whose precise function in viral morphogenesis is poorly understood. Both proteins are highly conserved across herpesviruses and likely perform similar functions in virion assembly and egress, with the gM/gN complex being essential for HCMV morphogenesis. To elucidate the function of the gM/gN complex in secondary envelopment, we employed a combination of viral mutants, siRNA knockdown experiments, and ultrastructural analyses. A detailed examination of the virion morphogenesis of a mutant virus with a cysteine-to-serine mutation in the cytoplasmic tail of gN (TB-gN-C123S) showed a defect in the initiation of secondary envelopment, as most capsids in TB-gN-C123S-infected cells were either not in contact with cytoplasmic membranes or, when near membranes, lacked signs of budding. The defect in initiation of secondary envelopment was associated with an accumulation of partially tegumented capsids in the peripheral region of the cytoplasmic viral assembly compartment (cVAC), whereas wild-type virus-infected cells predominantly accumulated enveloped capsids in the central area of the cVAC. Additionally, large protein aggregates were observed within and near the cVAC, often associated with non-enveloped capsids. A comparable ultrastructural phenotype, including altered capsid distribution, envelopment defect, and protein aggregation, was observed in wild-type virus-infected cells treated with siRNA against gM. Indirect immunofluorescence analysis confirmed the altered distribution of capsids in the cVAC in wild-type virus-infected cells with reduced or undetectable gM levels, resembling the pattern observed in TB-gN-C123S-infected cells. Further evidence underscoring the role of the gM/gN glycoprotein complex in viral morphogenesis was obtained by investigating gM- and gN-null mutants, which displayed the same altered capsid distribution observed in TB-gN-C123S infections and after siRNA knockdown of gM. Finally, the inhibition of palmitoylation using 2-bromopalmitate (2-BP) in wild-type virus-infected cells resulted in analogous defects, including an accumulation of partially tegumented capsids in the periphery of the cVAC and protein aggregates associated with capsids. In summary, our findings indicate a crucial role for the gM/gN complex in initiating the secondary envelopment of partially tegumented capsids and highlight the involvement of palmitoylation in this process. Defects in the initiation of secondary envelopment are associated with an altered spatial distribution of capsids within the cVAC. AUTHORS SUMMARYHuman cytomegalovirus (HCMV) is a widespread herpesvirus that can cause severe illness in newborns and immunocompromised individuals. Like other herpesviruses, HCMV assembles its infectious particles through a complex process that includes a final step called "secondary envelopment," in which the virus acquires its envelope. In this study, we investigated the role of two viral proteins, glycoprotein M (gM) and glycoprotein N (gN), which form a conserved complex across herpesviruses. Using genetic mutants, RNA interference, and electron microscopy, we found that the gM/gN complex is crucial for initiating secondary envelopment. When the function of gM or gN was disrupted, or when palmitoylation was chemically blocked, the capsids were unable to initiate budding into membranes, resulting in partially tegumented capsids that accumulated in the outer area of the cytoplasmic viral assembly compartment (cVAC). Our findings highlight the important role of the gM/gN complex and palmitoylation in HCMV assembly and suggest that assembly occurs in a spatially organized manner within the cVAC, offering new insights into how herpesviruses produce infectious particles.

microbiology↗

bioRxiv2025

NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia Telangiectasia

The cellular and molecular changes driving the neurological abnormalities associated with ataxia - telangiectasia (A-T) are not well understood. Here, we applied our proprietary Nuclear Enriched Transcript Sort sequencing (NETSseq) platform to investigate changes in cell type composition and gene expression in human cerebellar post-mortem tissue from A-T and control donors. Compared to single-nuclei technologies, NETSseq provided a more robust detection of genes with low abundance, a higher cell type specific expression pattern, and significantly lower levels of cross-contamination. We found dysregulation in neurotransmitter signaling in granule neurons, potentially underlying the impaired motor coordination in A-T. Astrocytes and microglia have evidence of accelerated aging, with astrocytes being characterized by neurotoxic signatures, while microglia showed activation of DNA damage response pathways. These findings highlight the importance of NETSseq as a resource for investigating mechanisms and biological processes associated with disease, providing high-sensitivity, cell-specific insights to advance targeted therapies for neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Unraveling Tyrosine-Kinase Inhibitor Resistance in NSCLC Cells via Same-cell Measurement of RNA, Protein, and Morphological Responses

Non-small cell lung cancer (NSCLC) frequently develops resistance to tyrosine kinase inhibitors (TKIs), limiting the long-term success of targeted therapies. A deeper understanding of resistance mechanisms at the molecular and cellular levels may enable the development of more effective treatment strategies. Here, we applied the Teton detection assay on the AVITI24 platform to measure concurrently RNA, protein, and cellular morphology in NSCLC cell lines treated with the TKIs gefitinib and osimertinib. This single-cell, multiomic analysis revealed distinct expression and morphological profiles between drug-sensitive and resistant cells, including differences in MAPK-related pathway activity. Stratifying responses at the single-cell level uncovered subtle responses not detectable in bulk measurements. We identified CDK4/6 activity as a route of cell survival under TKI treatment and demonstrated that co-treatment with the CDK4/6 inhibitor palbociclib enhanced TKI efficacy. The ability to measure multiomics and cellular morphology in the same cells opens new avenues for future studies aimed at improving personalized treatment strategies in NSCLC and overcoming the obstacles posed by drug resistance.

genomics↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗