Biology subjects

Ramirez, A.

Publications and source records attributed to Ramirez, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Lasting aversive consequences of a single dose of 4-hydroxytamoxifen

4-hydroxytamoxifen (4-OHT) is commonly used to facilitate activity-dependent recombination in neurons. Here we show that one dose of 4-OHT devalues alcohol, contexts, and tastants, indicating that experimental designs using 4-OHT should control for its aversiveness. Further, reactivation of 4-OHT-responsive neurons causes conditioned taste avoidance. An activity screen coupled with graph theoretical analysis identifies candidate brain areas mediating these effects. We suggest these areas could be therapeutic targets for treating addiction.

neuroscience↗

bioRxiv2026

Peptide additives reprogram the lipid nanoparticle corona and enhance gene delivery in a serum-free environment for lung epithelium

Lipid nanoparticles (LNPs) have become a clinical standard for systemically-administered nucleic acid drugs and vaccines, but the LNP pipeline for locally-delivered LNP therapies remains much less mature. Local delivery in lung represents a particularly compelling application space for DNA-LNP therapeutics, as local gene therapies could support sustained epithelial recovery and functional restoration in various lung diseases. However, locally-delivered DNA-LNPs face multiple barriers, including the limited availability of serum components that often support conventional LNP activity, and the additional delivery barriers posed by the nucleus. We generated hybrid peptide-lipid nanoparticles (hpLNPs) for pulmonary DNA delivery by using a core-shell assembly strategy to incorporate short histone-derived peptides, selected for their DNA-transport capacity, into a clinically inspired LNP formulation. In parallel, we evaluated serum pre-coating of LNPs as a strategy to boost hpLNP activity in the serum-poor airway environment. A peptide:DNA amine/phosphate (N/P) ratio of 0.9 was identified as the highest feasible ratio to permit peptide incorporation into hpLNPs while preserving DNA encapsulation efficiency at >90%, retaining hpLNP colloidal stability, and preserving the overall pKa for LNPs. At N/P = 0.9, hpLNPs showed markedly enhanced DNA delivery in alveolar lung cells, achieving up to a 17-fold increase in transgene expression compared to peptide-free LNPs. Transgene expression levels varied depending on serum concentration, with expression peaking in the presence of 6% serum. Furthermore, serum pre-coating was necessary to enable in vivo hpLNP activity following intratracheal administration in mice, yielding robust local GFP expression. Mechanistic studies in exosome-free serum revealed that peptide incorporation in the hpLNPs enhanced transgene delivery by increasing nanoparticle interactions with serum exosome components, resulting in significant enhancements to hpLNP uptake. Together, these findings identify nanoparticle- serum interactions as a critical determinant of LNP-mediated pulmonary DNA delivery and establish peptide incorporation and serum pre-coating as promising strategies to enable robust, localized gene transfer in serum-free environments.

bioengineering↗

bioRxiv2026

Drug Proarrhythmic Evaluation in a High Throughput Cardiac New Approach Methodology

Background and PurposeCardiotoxicity is a major cause for drug failure throughout the drug development process, with particular concern for action potential prolongation and arrhythmia. Hence, such liabilities are heavily considered during the early phases of drug design to pre vent dangerous compounds from progressing. New approach methodologies (NAMs) that efficiently examine this risk early in the discovery pipeline should help streamline drug development programs. We developed a cardiac NAM, a 384-well open bath platform consisting of cardiac tissue derived from human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes, enabling high-throughput drug screening while maintaining the structural and functional complexity of 3D cardiac micromuscles. MethodsWe dramatically increased throughput without compromising physiological relevance provided by the 3D micromuscle structure. Our 384-well open bath high-throughput platform allowed evaluation of multiple compounds at a time, enabling us to study the CiPA (comprehensive in vitro proarrhythmia assay) drug panel for proarrhythmia screening. We obtained phenotypic fingerprints of all 28 compounds (9 low, 11 intermediate, and 8 high arrhythmia risk; https://cipaproject.org) in dose-escalation studies around their respective clinical concentrations. The analysis was augmented with an in silico pipeline that used phenotypic biomarkers to invert data into a mathematical model of cellular currents to infer which ion channels were affected upon drug exposure, and then trained a ML model to predict channel block. Results and ConclusionsWe found accurate detection of arrhythmic potential for most of the compounds, and the in silico model inversions were consistent with published values of compound channel block. All the high risk compounds showed action potential duration (APD) prolongation coupled with either action potential abnormalities, early afterdepolarizations (EADs), or beat cessation. For the intermediate risk group, 9 out of 11 compounds caused APD prolongation alone or in combination with EADs while 2 others showed either beat cessation or beat rate change. Augmentation of APD analysis with detailed biophysical modeling and ML tools provided meaningful insight into the mechanisms involved in APD changes. Overall, our cardiac NAM allowed for fast and relevant screening for mechanistic understanding of APD prolongation and proarrhythmic activity, at massively increased throughput compared to other 3D micromuscle models. SummaryCardiotoxicity testing is critical in drug development to prevent arrhythmogenic side effects. Current stringent regulations have greatly reduced market withdrawals; however, these strict evaluations often lead to costly late-stage failures and loss of promising candidates as false positives. We developed a cardiac new approach methodology (NAM), a 384-well open bath cardiac micromuscle platform created from hiPSC-derived cardiomyocytes, enabling high-throughput drug screening while maintaining the structural and functional complexity of 3D cardiac micromuscles. Using the comprehensive in vitro proarrhythmia assay (CiPA) drug panel, we validated the system to accurately detect proarrhythmic potential. Our assay provided phenotypic fingerprints based on mechanical and electrophysiological biomarkers. Integration with computational modeling offered insights into multi-ion channel effects (MICE). Particularly, we identified sodium channel block contributions as a significant factor for poor risk prediction based on traditional parameters. The combined experimental and computational platform can enhance early drug screening, thereby reducing late-stage failures and promoting the progression of low-risk compounds with complex electrophysiological profiles.

pharmacology and toxicology↗

bioRxiv2026

Tracing cell communication programs across conditions at single cell resolution with CCC-RISE

Cell-cell communication (CCC) mediates coordinated cellular activities that vary dynamically across time, location, and biological context. While various tools exist to infer CCC, they typically aggregate data according to pre-defined cell types, obscuring critical single-cell heterogeneity. Furthermore, because signaling pathways and cell populations operate in a coordinated manner, an integrative analytical approach is essential. To address these challenges, we developed CCC-RISE, an extension of the tensor-based method Reduction and Insight in Single-cell Exploration (RISE). CCC-RISE identifies integrative patterns of single-cell variation by deconvolving communication into interpretable modules defined by unique sender cells, receiver cells, ligands, and condition associations. We applied this framework to a COVID-19 cohort with varying disease severity and a lung transplant cohort with acute allograft dysfunction. In both contexts, CCC-RISE successfully identified disease-relevant communication programs and traced them to specific cellular subpopulations, often crossing conventional cell-type boundaries. This approach offers a robust pipeline enabling the identification of disease-relevant signaling subpopulations that are invisible to aggregate methods. HighlightsO_LICCC-RISE enables integrative analysis of cell-cell communication across multiple conditions at single-cell resolution C_LIO_LICCC-RISE deconvolves signaling patterns into modules defined by their sender cells, receiver cells, LR pairs, and experimental conditions/samples C_LIO_LIAnalysis at single-cell resolution uncovers signaling activity within and across conventional cell types C_LI

systems biology↗

bioRxiv2026

Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at the PICALM-EED locus for Alzheimer Disease

ObjectiveBoth the phosphatidylinositol binding clathrin assembly protein gene (PICALM) and the embryonic ectoderm development gene (EED) have been implicated as causal genes driving a genome-wide association for Alzheimer disease (AD) risk. We employed a new virtual approach using genome-wide chromatin interactions (Hi-C) called enhanced Hi-C Capture Analysis (eHiCA) to identify the genes and regulatory regions that are driving this important AD risk association. MethodsHi-C data from the frontal cortex of eight AD patients, as well as inducible pluripotent stem cell-derived microglia and spheroids of AD and control patients were used. We applied 14 eHiCA baits each containing a GWAS SNP to identify the cis regulatory interactions in this GWAS locus at a 5kb resolution. ResultsThe baits derived from the GWAS associated haplotype primarily interacted with the PICALM promoter and the large cis-regulatory elements cluster (CREe) lying upstream of the EED promoter. The EED promoter interacts with PICALM gene body and promoter region but not directly with the associated risk haplotype. Although the AD-associated variants segregate together as a haplotype in the population, each bait exhibited distinct functional chromatin interactions. InterpretationThe PICALM gene is the primary driver of the association in microglia along with the CREe locus. Different SNPs in a segregating haplotype can display different physical Hi-C interactions. This study demonstrates that eHiCA can help resolve the casual genes driving complex GWAS associations, opening new pathways to study Alzheimer disease and other disorders.

genomics↗

bioRxiv2026

Evolutionary rate covariation across malaria parasite species enables inference of protein interactions

Despite publication of the Plasmodium falciparum reference genome over 20 years ago, one-third of its genes remain functionally unannotated, and information is limited for many others. Proteins that act in the same pathway or complex tend to experience similar shifts in evolutionary pressure, such that correlated constraints across species can indicate co-functional proteins. To investigate this connection, we calculated relative evolutionary rates across the genome on a phylogeny of 22 Plasmodium species and assigned each protein-protein pair a score representing the strength of evolutionary rate covariation (ERC). We show that known pathways and interacting proteins across lifecycle stages in Plasmodium have strong ERC signals. By scanning genome-wide for additional proteins showing high ERC with established interacting proteins, we find enrichment of stage expression and physically interacting protein pairs supporting new candidate functions for proteins. More generally, we demonstrate the utility of ERC to prioritize proteins for hypothesis-driven functional follow up by showing that a protein with little functional characterization (PF3D7_0811600) shows high ERC and co-localizes with high molecular weight rhoptry proteins 2 and 3 (RhopH2 and RhopH3), which form an ion channel that enhances parasite permeability of infected red blood cells. The ERC matrix can be queried to extract Plasmodium proteins showing high ERC with any protein of interest to prioritize candidate genes and accelerate discovery of novel functional connections.

evolutionary biology↗

bioRxiv2025

A single-cell spatial transcriptomic census of human skin anatomy

The skin is the largest human organ and a site of significant disease burden, yet its cellular and molecular organization across the body are largely undefined. Here, we construct a spatially-resolved single-cell atlas of 1.2 million cells from normal adult human skin to localize 45 cell types across 15 anatomic sites. We define principles of organ-wide cell composition, including axes of cell diversity and specialization, and distinguish site-enriched cell types. Each body site is comprised of 10 multicellular neighborhoods that define cell-cell communication. Notably, we identify a perivascular neighborhood enriched for immune-stromal crosstalk with features resembling a homeostatic immune niche similar to skin-associated lymphoid tissue. Finally, mapping these neighborhoods onto skin disease reveals pathogenic neighborhood disruptions, including pan-disease immune alterations in the perivascular neighborhood. We present a framework charting the skins multiscale spatial organization across a molecular to macroanatomic scale. This work advances our understanding of organ-wide skin cellular organization and communication, and its architectural disruption in disease. HIGHLIGHTSO_LIHuman skin MERFISH spatial atlas of 1.2 million cells from 114 samples and 22 donors C_LIO_LICellular diversity varies along a central to peripheral body site spatial axis C_LIO_LI10 multicellular neighborhoods define skin microanatomy and homeostatic interactions C_LIO_LIHuman skin diseases feature spatial and transcriptional neighborhood remodeling C_LI

genomics↗

bioRxiv2025

The Neuromuscular system of Chironomus vitellinus (Diptera: Chironomidae)

Chironomids are important laboratory model organisms used to assess toxicity in freshwater environments. Cell and tissue features are not commonly used as chironomid markers to detect toxicity, but they could be extremely helpful in identifying acute and chronic effects of pollutants. The nervous system is an excellent cellular candidate since it is reactive to toxic substances. However, a detailed description of the chironomid nervous system is required prior to considering it as a candidate for a cellular toxicity marker. The present study describes the central ganglia, nerves, axons, and the neuromuscular system of Chironomus vitellinus (Freeman, 1961) to facilitate its use as a model organism in environmental studies. We find that the structure of the C. vitellinus central nervous system is identical to that observed in other Chironomus larvae. We then focused our study on the first abdominal segment and labeled the 31 hemi-segmental muscles according to a nomenclature based on their position and orientation. We also characterized their innervation and assigned the nerves a nomenclature based on their terminals location in the muscle tissue. Finally, we investigated the neuromuscular junctions (NMJs) throughout this segment and defined four types of NMJs illustrating their great variability in size and shape. We selected a model NMJ, VEL 2, and quantified its mean bouton number and muscle size. Together with documenting a neurobiological system that could be informative to insects comparative biology, these results could help establish the Chironomus NMJ as an aquatic toxicity marker.

neuroscience↗

bioRxiv2025

Insight into the genetic network governing long-stalked glandular trichome development in Nicotiana tabacum

Glandular trichomes play a pivotal role in plant defense against various biotic and abiotic stresses. To unravel the genetic network driving glandular trichome development in Nicotiana tabacum, we employed a transcriptional switch-based approach using heterologous expression of AmMIXTA, a MYB transcription factor from Antirrhinum majus. Through comprehensive RNA-seq analysis of transgenic tobacco seedlings where long-stalked glandular trichome development was induced in aerial parts, we identified a suite of differentially expressed genes, including several transcription factors, shedding light on the early transcriptional cascade governing this developmental process. Moreover, through confocal live cell imaging of transcriptional reporter lines, interaction studies and DAP-seq assays, we confirmed the involvement of NtZFP8, a gene identified in our study, in long-stalked glandular trichome development. Our findings support a model in which NtZFP8 regulates a gene network essential for this developmental process. This study underscores the effectiveness of our approach in decoding the regulatory landscape of glandular trichome development in N. tabacum and provides a valuable framework for future functional investigations. Key MessageGlandular trichomes are essential for plant defense. Using a transcriptional switch-based approach in Nicotiana tabacum, we identified key regulators, including NtZFP8, which controls long-stalked trichome development. Our study establishes a foundation for future functional analyses of candidate genes uncovered through this approach.

plant biology↗

bioRxiv2025

Two-timepoint assays of neural responses increase the sensitivity and specificity of single-cell whole-brain activity screens

Current approaches for surveying whole brains for neurons activated during a particular state typically rely on immediate early gene (IEG) expression. However, IEG expression is variable across subjects and brain areas, demanding large sample sizes. Further, it cannot determine if the same or different neurons respond to two events. To overcome these issues, we present a whole-brain screening method utilizing transgenic mice to label neurons activated at two timepoints. An imaging and analysis pipeline surveys activity in ~500 brain areas in different conditions. Compared to IEG methods, this approach reduces required sample sizes and enhances sensitivity and specificity. Finally, graph theoretical analyses are utilized to identify key circuit nodes - brain areas whose activity correlates with activity in other areas in a state-dependent manner. We validate this method by surveying whole-brain activity during hunger and satiety, and by investigating neural circuits activated by the GLP1 agonist semaglutide used to treat obesity.

neuroscience↗

bioRxiv2025

A Ras-like GTPase in African trypanosomes

Small Ras-like GTPases are conserved across eukaryotes and mediate many functions. Trypanosoma brucei encodes only three putative open reading frames belonging to Ras and Rho subfamilies, all highly divergent from other taxa. We investigated the most Ras-like gene product in T. brucei, TbRlp, evaluating essentiality, location and impact of blocking the GDP/GTP cycle. TbRlp is expressed in both life stages, with a clear fitness contribution in bloodstream forms in in vitro culture, without a specific block to the cell cycle or clear morphological defect. Overexpression of TbRlp and mutant forms results in moderate disruption of the cell cycle and altered proliferation indicating that GTP/GDP cycling and expression levels of these forms of TbRlp are important to proliferation. Epitope-tagged TbRlp is located predominantly on structures in the posterior of the cell, and suggesting the late endosomal system. Analyses also indicates a link between cell density and levels of TbRlp in the BSF, with a decrease in TbRlp protein but not RNA upon increased cell density. These data suggest that TbRlp is important in control of proliferation and opens possibilities for future research.

cell biology↗

bioRxiv2025

Inflammation modulates lymph node biomechanics in a sex-dependent manner

Lymph nodes are highly specialized immune organs that orchestrate the adaptive immune response. In the lymph nodes, naive B and T lymphocytes encounter cognate antigens, sparking their activation and response to foreign substances. Lymph nodes grow in response to an immune challenge, at least in part to accommodate increased numbers of infiltrating and proliferating B and T lymphocytes. This behavior is supported by a robust three-dimensional network of extracellular matrix (ECM) fibers and fibroblastic reticular cells (FRCs). ECM fibers and FRCs work synergistically to alternate stretching and contractile forces between them allowing the lymph node to maintain structural integrity during rapid tissue reconstruction. These changes ultimately alter the material properties of the lymph node, which can impact cell migration, proliferation, and differentiation. Recent work has investigated the physiological implications of the changing lymph node microenvironment; however, the biophysical properties of the lymph nodes during these changes remain largely unexplored. Here, we use multiple particle tracking microrheology (MPT), a minimally invasive nanoparticle-based technique to investigate the biophysical properties (elastic/loss moduli, microviscosity, pore size) of lymph nodes post inflammatory stimulus. Our results highlight mechanical changes both during the initial phases of the acute inflammatory response and upon resolution of inflammation, a topic that is relatively understudied. We show that B and T cell rich areas exhibit comparable changes in biomechanical properties over time, suggesting that they restructure in a similar fashion during acute inflammation. Additionally, for the first time, we show that biological sex modulates lymph node biomechanics in acute inflammation: Lymph nodes from female mice showed a [~]20-fold increase in elastic and loss moduli at peak inflammation, while lymph nodes from male mice had a [~]5-fold decrease in both moduli. Additionally, lymph nodes from female mice appeared to permanently remodel during the resolution of acute inflammation resulting in the maintenance of an overall higher elastic and loss modulus, while lymph nodes from male mice returned to the biomechanics of untreated lymph nodes. We also found that at least some of the changes in biomechanical properties were correlated with changes in ECM materials in the lymph nodes, suggesting a structure-function relationship. Overall, our studies provide key insights into how biomechanical properties in lymph nodes are altered during inflammation, a previously unstudied area, and lay the foundation for structure-function relationships involved in immune response. Additionally, we demonstrate a robust technique for the analysis of the lymph node interstitial tissue properties and how they vary with inflammatory stimuli.

bioengineering↗

bioRxiv2024

Mapping cell-cell fusion at single-cell resolution

Cell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo ( CMDuo), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to randomly generated nucleotide barcodes. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple-negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response.

systems biology↗

bioRxiv2024

Dysfunction of the episodic memory network in the Alzheimer's disease cascade

Alzheimers disease (AD) is a major cause of dementia and cognitive decline. Here we assessed how episodic memory circuit dysfunction, a hallmark of AD, is related to the longitudinal cascade of AD biomarkers, neurodegeneration and cognition using data from the DZNE Longitudinal Cognitive Impairment and Dementia study. This data set is unique by including over 1000 longitudinal functional magnetic resonance imaging (fMRI) measurements during episodic memory encoding. We leveraged a disease progression model (DPM) to obtain AD progression scores. Voxel-wise analyses revealed widespread loss of deactivation (hyperactivation) and activation (hypoactivation) with increasing disease stage. Hyperactivation trajectories were nonlinear and visually preceded trajectories of cognition. Overall, hyperactivation was independently associated with co-occurrence of amyloid- and tau-positivity and neurodegeneration, suggesting synaptic dysfunction and neurodegeneration as two independent drives of cognitive decline. Our results therefore provide evidence for a critical time window in which pharmacological treatments targeting the synapse may improve cognition.

neuroscience↗

bioRxiv2024

Protective variant in PLCgamma2 mitigates Alzheimer's disease associated pathology via enhancing beneficial microglia functions

BackgroundPLC{gamma}2-P522R (phospholipase C gamma 2, proline 522 to arginine) is a protective variant that reduces the risk for late onset Alzheimers disease. Recently, it was shown to decrease {beta}-amyloid pathology in 5XFAD mouse model of AD. In this study, our goal was to investigate the protective functions of PLC{gamma}2-P522R variant in a less aggressive mouse model of AD as well as to assess the underlying mechanisms at the molecular and cellular level using mouse and human microglia models. MethodsThe effects of the protective PLC{gamma}2-P522R variant on microglia activation, AD-related {beta}-amyloid and neuronal pathologies, as well as behavioral changes were investigated in PLC{gamma}2-P522R knock-in mice crossbred with APP/PS1 AD model mice. Transcriptomic, proteomic, and functional studies were carried out in cultured and acutely isolated adult PLC{gamma}2-P522R mouse microglia to study molecular mechanisms. Finally, microglia-like cell models generated from blood and skin biopsy samples of the PLC{gamma}2-P522R variant carriers were employed to translate the key findings to human cells. ResultsOur results demonstrate that the PLC{gamma}2-P522R variant reduced brain {beta}-amyloid plaque burden of APP/PS1 mice. Simultaneously, PLC{gamma}2-P522R variant increased non-proinflammatory microglia activation and microglia clustering around {beta}-amyloid plaques, leading to reduced {beta}-amyloid plaque-associated neuronal dystrophy. In cultured mouse primary microglia, PLC{gamma}2-P522R variant decreased accumulation of large lipid droplets, reduced cell stress, and increased acute response to strong inflammatory stimuli. Transcriptomic and proteomic analyses in acutely isolated adult mouse microglia as well as in human monocyte-derived microglial cells showed that PLC{gamma}2-P522R upregulates mitochondrial fatty acid oxidation and downregulates inflammatory/interferon signaling pathways. Accordingly, PLC{gamma}2-P522R increased mitochondrial respiration in iPSC-derived microglial cells. ConclusionsTogether, these findings suggest that PLC{gamma}2-P522R variant exerts protection against AD-associated {beta}-amyloid and neuronal pathologies via enhancing microglial barrier formation around {beta}-amyloid plaques and suppressing pro-inflammatory activation. Observed changes in fatty acid metabolism and mitochondrial flexibility as well as the downregulation of genes involved in inflammatory signaling pathways suggest that these protective effects of the PLC{gamma}2-P522R variant are mediated through an anti-ageing mechanism.

neuroscience↗

bioRxiv2024

Delayed post-juvenile moult in malaria-infected European blackcaps

Parasites have their strongest impact on fitness when host defences limit the quantity of resources available for other critical life-history stages, such as development, breeding or migration. One greatly neglected stage that could be altered by parasites is the post-juvenile moult (PJM) of birds, through which inexperienced yearlings replace their weak and fast-generated juvenile feathers by adult-like feathers. The earlier juvenile birds complete PJM, the earlier they will be prepared to withstand forthcoming adverse conditions, especially if they migrate short after moulting. We used data from 435 juvenile European blackcaps (Sylvia atricapilla) sampled during three years in 26 localities spanning the wide range of environmental conditions across Iberian Spain to test whether haemosporidian infections (presence and abundance in blood of parasites of the genera Haemoproteus, Plasmodium and Leucocytozoon) were related to delayed PJM. Controlling for body condition, sex, year and date of capture, infected blackcaps (single-infected or coinfected) had lower moult scores indicative of delayed moult, especially when birds had Plasmodium infections or higher intensity of Haemoproteus parasites. Our results broaden the range of fitness costs that haemosporidian parasites may have on birds, as delayed plumage maturation prolongs the period during which juvenile birds lack a fully functional plumage.

ecology↗

bioRxiv2024

Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2

Effective and scalable exploration and analysis tools are vital for the extraction of insights from large-scale single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that Reduction and Insight in Single-cell Exploration (RISE), an adaptation of the tensor decomposition method PARAFAC2, enables the dimensionality reduction and analysis of single-cell data across conditions. We demonstrate the benefits of RISE across two distinct examples of single-cell RNA-sequencing experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. RISE enables straightforward associations of gene variation patterns with specific patients or perturbations, while connecting each coordinated change to single cells without requiring cell type annotations. The theoretical grounding of RISE suggests a unified framework for many single-cell data modeling tasks. Thus, RISE provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts. HighlightsO_LIRISE enables tensor-based analysis of single-cell experiments across conditions. C_LIO_LIRISE separates condition-specific effects from cell-to-cell variation. C_LIO_LIRISE provides intuitive isolation of patterns into condition-, cell-, and gene-specific patterns. C_LI

systems biology↗

bioRxiv2024

Development, validation and application of an LC-MS/MS method quantifying free forms of the micronutrients queuine and queuosine in human plasma using a surrogate matrix approach

Queuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside exclusively synthesized by bacteria. This micronutrient and its respective nucleobase form queuine (q) are salvaged by humans either from gut microflora, or digested food. Depletion of Q-tRNA in human or mouse cells causes protein misfolding that triggers endoplasmic reticular stress and activation of the unfolded protein responses. In vivo, this reduces neuronal architecture of the mouse brain affecting learning and memory. Herein, a sensitive method for quantifying free q and Q in human blood was developed, optimised and validated. After evaluating q/Q extraction efficiency in several different solid-phase sorbents, Bond Elut PBA (phenylboronic acid) cartridges were found to have the highest extraction recovery for q (82%) and Q (71%) from pooled human plasma. PBS with 4% BSA was used as surrogate matrix for method development and validation. An LC-MS/MS method was validated across the concentration range of 0.0003 - 1 {micro}M for both q and Q, showing excellent: linearity (r2 = 0.997 (q) and r2 = 0.998 (Q)), limit of quantification (0.0003 {micro}M), accuracy (100.39% - 125.71%) and precision (CV% < 15.68%). In a sampling of healthy volunteers (n = 44) there was no significant difference in q levels between male (n = 14; mean = 0.0068 {micro}M) and female (n = 30; mean = 0.0080 {micro}M) participants (p = 0.50). Q was not detected in human plasma. This validated method can now be used to further our understanding of the role of q/Q in nutrition, physiology and pathology.

biochemistry↗