Biology subjects

Hill, B.

Publications and source records attributed to Hill, B..

At least 19 recordsLinked to original sources

bioRxiv2026

IL-1β and TNF drive endothelial dysfunction and coagulopathy in acute COVID-19.

Vascular dysfunction and coagulopathy are hallmarks of severe COVID-19. How SARS-CoV-2 infection drives endothelial dysfunction, despite the virus not infecting or replicating in endothelial cells, remains controversial. Here, we used an in vitro co-culture model of the human pulmonary epithelial-endothelial cell barrier to investigate which inflammatory mediators drive endothelial dysfunction during SARS-CoV-2 infection. SARS-CoV-2 infection of primary human bronchial epithelial cells increased adjacent endothelial cell expression of the leukocyte adhesion marker ICAM-1, disrupted endothelial VE-cadherin junctions, promoted endothelial cell death, and promoted platelet adherence to gaps in the endothelial monolayers. Dexamethasone treatment rescued these dysregulated endothelial phenotypes in infected co-cultures, confirming that inflammatory signalling was the primary driver of SARS-CoV-2-induced endothelial dysfunction. Specifically, epithelial-derived TNF and IL-1{beta} promoted endothelial dysfunction, as inhibition of TNF or IL-1R signalling blocked SARS-CoV-2-induced endothelial dysfunction in co-cultures. SARS-CoV-2-infected wild-type mice, but not TNF, IL-1{beta}, or TNF/IL-1{beta}- deficient mice, displayed increased endothelial ICAM-1 expression, while an anti-IL-1{beta} monoclonal antibody prevented SARS-CoV-2-induced ICAM-1 expression and fibrin deposition in aged K18-ACE2 mice. Our data indicate that TNF and IL-1{beta} are the specific cytokines that drive multiple aspects of endothelial dysfunction during acute SARS-CoV-2 infection, and that inhibiting their signalling pathways may provide therapeutic benefit in preventing vascular complications of COVID-19.

cell biology↗

bioRxiv2026

E-Selectin Orchestrates IL-1B-Dependent Neuroinflammation via NLRP3 in Vincristine-Induced Neuropathy

Vincristine-induced peripheral neuropathy (VIPN) is a frequent and dose-limiting complication of cancer therapy, yet the upstream mechanisms coupling vascular activation to neuroinflammation remain poorly defined. Here we identify E-selectin as a critical orchestrator of vincristine-induced neuropathy. Systematic interrogation of endothelial adhesion molecules in a murine model of VIPN revealed that blockade of E-selectin, but not ICAM-1, PECAM-1 or P-selectin, completely prevented mechanical hypersensitivity and markedly reduced F4/80 immune cell accumulation in dorsal root ganglia and peripheral nerves. Genetic deletion of E-selectin conferred equivalent protection, despite the absence of structural loss of intraepidermal or myelinated fibres, indicating a predominantly functional neuroimmune pathology. Spatial transcriptomics demonstrated that vincristine induces a conserved stress and neuroinflammation-associated transcriptional programme in dorsal root ganglia, with immune and stromal populations acting as dominant signalling hubs. Genetic or pharmacological perturbation of E-selectin did not abolish injury-associated pathways but redistributed cell-cell communication networks, reducing immune-cell dominance and reshaping interferon and metabolic signalling states without inducing Sele expression. Mechanistically, E-selectin exerted non-canonical effects beyond endothelial adhesion. Local E-selectin administration was sufficient to induce macrophage-dependent mechanical hypersensitivity that was abolished in Fut4/7-deficient mice and following phagocyte depletion. In macrophages, E-selectin enhanced vincristine-driven NF-{kappa}B activation, NLRP3 inflammasome assembly and IL-1{beta} release. Together, these findings position E-selectin as an upstream regulator of IL-1{beta}-dependent neuroinflammation in VIPN and identify selective targeting of E-selectin-mediated immune-neuron interactions as a therapeutic strategy for chemotherapy-induced neuropathy.

neuroscience↗

bioRxiv2026

Improving Turnaround Times with Artificial Intelligence in Microbiology

This dual-center study evaluated the impact of artificial intelligence (AI) on urine culture turnaround times in Canadian diagnostic laboratories employing full microbiology laboratory automation. Data were collected before and after the implementation of PhenoMATRIX (PM), an AI-based software designed to support culture sorting and result interpretation. In both a low-volume tertiary care hospital and a high-volume community laboratory, PM reduced the time to final culture reporting, with decreases of approximately 1.5 hours and 3.9 hours, respectively. Implementation of PM+, which automatically releases defined results to patient charts, further improved turnaround time. These findings indicate that microbiology laboratories with full laboratory automation can achieve further improvements in turnaround time by integrating AI-culture assessment and results release.

microbiology↗

bioRxiv2025

Cannabidiol as a Prophylactic Agent Against Glioblastoma Growth: A Preclinical Investigation

PurposeGlioblastoma (GBM) is one of the most aggressive brain tumors, with limited treatment options and poor outcomes due to frequent relapse after surgery. This study aims to investigate whether pretreatment with inhaled cannabidiol (CBD) can inhibit GBM growth in a preclinical murine model. Specifically, we hypothesize that CBD pretreatment may reduce tumor progression and modulate the tumor microenvironment. MethodsC57BL/6 mice were pretreated with inhaled CBD for either 3 or 14 days, or a placebo, followed by intracranial implantation of glioblastoma cells. Tumor growth, immune checkpoint expression (IDO, PD-L1), and key biomarkers (MGMT, Ki67) were assessed to determine the impact of CBD pretreatment on tumor progression and the immune microenvironment. ResultsThe 14-day CBD pretreatment significantly reduced tumor growth compared to both the placebo and 3-day CBD groups. Additionally, this group showed lower expression of immune checkpoints (IDO, PD-L1) and reduced levels of MGMT and Ki67, suggesting enhanced tumor suppression. These results indicate that prolonged CBD pretreatment modulates the tumor microenvironment and may improve tumor control and reduce relapse risk. ConclusionThis study demonstrates that inhaled CBD pretreatment significantly inhibits GBM growth in a preclinical model. CBDs ability to reduce immune checkpoint expression and key biomarkers associated with tumor progression suggests that it could be an effective strategy for enhancing the efficacy of GBM therapies and potentially improving post-surgical outcomes. Further research is required to investigate its clinical potential and mechanisms of action.

cancer biology↗

bioRxiv2025

Accurately modelling RNase H-mediated antisense oligonucleotide efficacy

Antisense oligonucleotides (ASOs) are a powerful class of drugs with the potential to treat a wide range of human diseases. However, the prediction of ASO efficacy remains challenging, as large-scale and costly experimental screens are typically required to identify optimal candidates for a specific therapeutic target. To address this challenge, we compiled ASO Atlas, a database comprising 188,521 RNase H-mediated ASO sequences targeting 334 unique genes with corresponding knockdown efficacy measurements extracted from published patents. Using ASO Atlas, we trained OligoAI, a deep learning model capable of jointly modelling RNA target context, ASO sequence, sugar and backbone chemistries, and dosage to predict in vitro efficacy. We experimentally validated OligoAI by targeting KCNT2, achieving a 5.72-fold reduction in screening effort compared to random selection. ASO Atlas provides the first systematic resource to rigorously evaluate hypotheses regarding key parameters in ASO design, including sequence composition, chemical modifications, and target region selection. Both ASO Atlas and OligoAI have been made freely accessible through an online web-tool with the aim of facilitating the accelerated optimisation of ASO design.

bioinformatics↗

bioRxiv2025

Rethinking Alzheimer's: Harnessing Cannabidiol to Modulate IDO and cGAS Pathways for Neuroinflammation Control

Alzheimers disease has traditionally been associated with amyloid-{beta} plaques, but growing evidence underscores the role of neuroinflammation in disease progression. The autoimmune hypothesis of Alzheimers disease suggests chronic inflammation and immune dysfunction contribute to neuronal damage, making modulation of immune responses a promising therapeutic strategy for the disease. Cannabidiol, a phytocannabinoid with anti-inflammatory properties, may offer therapeutic potential. This study explores how cannabidiol influences the Indoleamine 2,3-dioxygenase (IDO) and cyclic GMP-AMP synthase (cGAS) pathway, a key regulator of neuroinflammation in Alzheimers disease. Using the 5XFAD transgenic mouse model of Alzheimers disease, we administered cannabidiol via inhalation. We assessed immune markers, including Indoleamine 2,3-dioxygenase and cyclic GMP-AMP synthase, through flow cytometry, immunofluorescence staining, and gene expression analysis. Cytokine levels and neuroinflammatory responses were evaluated, and protein-protein interactions within the Indoleamine 2,3-dioxygenase/cyclic GMP-AMP synthase pathway were analyzed using the STRING database. Cannabidiol treatment significantly reduced Indoleamine 2,3-dioxygenase and cyclic GMP-AMP synthase expression, correlating with lower levels of pro-inflammatory cytokines, including Tumor Necrosis Factor-alpha, Interleukin-1 beta, and Interferon-gamma. Bioinformatics analysis identified potential interactions between cannabidiol and immune targets such as Protein Kinase B (AKT1), Transient Receptor Potential Vanilloid 1, and G-protein coupled receptor 55, suggesting a multi-targeted therapeutic effect. These findings support cannabidiol as a potential monotherapy or adjunctive treatment for Alzheimers disease, targeting neuroinflammatory pathways, particularly the Indoleamine 2,3-dioxygenase/cyclic GMP-AMP synthase axis. Further studies are needed to explore its full therapeutic potential.

immunology↗

bioRxiv2024

Endothelial c-Src mediates neovascular tuft formation in Oxygen-Induced Retinopathy

IntroductionVascular retinopathy, characterised by abnormal blood vessel growth in the retina, frequently results in vision impairment or loss. Neovascular tufts, a distinctive pathological feature of this condition, are highly leaky blood vessel structures, exacerbating secondary complications. Despite their clinical significance, the mechanisms underlying tuft development are not fully elucidated, posing challenges for effective management and treatment of vascular retinopathy. In this study, we investigate the role of c-Src in neovascular tuft formation. Although c-Src has been acknowledged as a pivotal regulator in developmental angiogenesis within the retinal vasculature, its specific role in governing pathological retinal angiogenesis remains to be fully understood. MethodsWe utilised the Oxygen-Induced Retinopathy (OIR) model to induce the formation of neovascular tufts in both Cre-mediated vascular specific c-Src knockout mice and their wildtype littermates. Subsequently, we conducted high-resolution imaging and analysis of isolated retinas, to elucidate the precise role of c-Src in the formation of vascular tufts. Resultsc-Src depletion demonstrated a significant reduction in the formation of neovascular tufts within the OIR model, underscoring the pivotal role of c-Src in pathological retinal angiogenesis. Notably, this decrease in tuft formation was observed independently of any alterations in cell death, cell proliferation or cell adhesion and the absence of c-Src did not impact tuft pericyte coverage and junctional morphology. ConclusionThese findings underscore the critical role of c-Src in the pathogenesis of neovascular tufts in vascular retinopathy. Understanding the molecular mechanisms involving c-Src may offer valuable insights for the development of targeted therapies aimed at mitigating vision-threatening complications associated with retinopathy.

pathology↗

bioRxiv2024

Development of a qPCR assay and a LAMP assay for Verticillium longisporum detection and a triplex qPCR assay for simultaneous detection of V. longisporum, Leptosphaeria biglobosa and L. maculans from canola samples

Verticillium wilt, Verticillium stem striping, and Verticillium stripe, are common disease names that all denote infection caused by Verticillium longisporum, on canola, or other Brassica crops. In this study, a quantitative PCR (qPCR) assay and a loop-mediated isothermal amplification (LAMP) assay were developed for the detection of V. longisporum from canola stem samples. Both assays are specific to V. longisporum at the species level and ubiquitous at the strain level. The low limit for positive detection of the two assays is 1 pg fungal DNA in a 20-{micro} L reaction or 1,400 fungal cells in 100-mg plant tissue. The qPCR assay was combined with the duplex qPCR assay for the two blackleg pathogens, Leptosphaeria biglobosa and L. maculans to constitute a triplex qPCR system for simultaneous detection of all three pathogens. The usefulness of this triplex qPCR system was verified on canola samples collected from various locations in Alberta, Canada. Using this triplex qPCR system, V. longisporum was detected from one sample, while the two blackleg pathogens were detected at higher frequencies. Since it is sometimes difficult to differentiate Verticillium stripe and blackleg on Alberta canola samples based on visual symptoms, the triplex qPCR system is an important tool for the detection of V. longisporum, especially when its presence is masked or obscured by symptoms of blackleg.

microbiology↗

bioRxiv2023

Epigenetic field defect discriminates normal tissues from healthy and tumor-bearing kidneys

BackgroundThe detection of alterations in DNA methylation (DNAm) in normal human tissues may provide molecular insights for cancer development, the estimation of personal cancer risk, and a basis for early diagnosis of malignancies to reduce cancer lethality. Thus, whether DNAm allows discrimination between healthy normal and normal tumor-adjacent renal tissues is an important question. MethodsDNAm of loci in the LINE1 repetitive sequence and ANKRD34B, NHLH2, TBR1, and ZIC1 was measured in a total of 493 tissue samples representing 342 normal autopsy and 151 histopathological normal tumor-adjacent renal tissues by pyro-sequencing a total of 22 CpG sites. ResultsUnsupervised k-means clustering demonstrated a significant imbalance of tissue samples in three stable tissue clusters. Random forest classification demonstrated discrimination of normal and normal tumor-adjacent renal tissues with a median area under the ROC curve of 0.81 (p=2.7x10-9, diagnostic odds ratio 10.4). Variable importance analysis revealed CpG sites in LINE1 and ANKRD34B as the most important model contributors. ConclusionsDNAm alterations in normal tissues allow detection of renal cancer with high diagnostic efficiency, defining a DNAm field effect in the kidney. The methylation signature may serve as a basis for an epigenetic DNAm clock permitting estimation of individual renal cancer risk.

cancer biology↗

bioRxiv2023

c-Src induced vascular malformations require localised matrix degradation at focal adhesions

Endothelial cells lining the blood vessel wall communicate intricately with the surrounding extracellular matrix, translating mechanical cues into biochemical signals. Moreover, vessels require the capability to enzymatically degrade the matrix surrounding them, to facilitate vascular expansion. c-Src plays a key role in blood vessel growth, with its loss in the endothelium reducing vessel sprouting and focal adhesion signalling. Here, we show that constitutive activation of c-Src in endothelial cells results in rapid vascular expansion, operating independently of growth factor stimulation or fluid shear stress forces. This is driven by an increase in focal adhesion signalling and size, with enhancement of localised secretion of matrix metalloproteinases responsible for extracellular matrix remodelling. Inhibition of matrix metalloproteinase activity results in a robust rescue of the vascular expansion elicited by heightened c-Src activity. This supports the premise that moderating focal adhesion-related events and matrix degradation can counteract abnormal vascular expansion, with implications for pathologies driven by unusual vascular morphologies.

cell biology↗

bioRxiv2022

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

BackgroundThe Human Cell Atlas resource will deliver single cell transcriptome data spatially organised in terms of gross anatomy, tissue location and with images of cellular histology. This will enable the application of bioinformatics analysis, machine learning and data mining revealing an atlas of cell types, sub-types, varying states and ultimately cellular changes related to disease conditions. To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms. MethodsWe describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut. This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patients CT scan where the gut has been segmented. ResultsThe outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. All data and software is fully open-source and available online. ConclusionsSmall and large intestines have a natural "gut coordinate" system best represented as a 1D centreline through the gut tube, reflecting functional differences. Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. This permits users to accurately locate samples for data comparison.

bioinformatics↗

bioRxiv2022

Cas9+ conditionally immortalized neutrophil progenitors as a tool for genome wide CRISPR screening for neutrophil differentiation and function

Neutrophils are short-lived cells of the innate immune system that play numerous roles in defense against infection, regulation of immune responses, tissue damage and repair, autoimmunity, and other non-communicable diseases. Understanding neutrophil function at a mechanistic level has been hampered by the difficulty of working with primary neutrophils, which die rapidly upon isolation, and the relative paucity of neutrophil cell lines. Murine neutrophil progenitors that are immortalized with estrogen-regulated expression of Hoxb8 differentiate into neutrophils upon withdrawal of estrogen and facilitate the quantitative production of neutrophils in vitro. Here we report the creation of a Cas9+ER-Hoxb8 neutrophil progenitor cell line that enables both forward and reverse genetic analysis of neutrophils for the first time. By editing progenitors via transduction with sgRNAs, and then withdrawing estrogen, Cas9 edited neutrophils are produced with high efficiency. Importantly, neutrophil differentiation of edited progenitors occurs both in vitro in cell culture and when transferred into murine recipients. To demonstrate the utility of Cas9+ER-Hoxb8 progenitors for forward genetics, we performed a pooled CRISPR screen to identify factors required for survival during neutrophil differentiation. This screen identified hundreds of genes both negatively and positively selected under differentiation conditions. One of the top hits from this screen was Cebpe, a transcription factor known to be required for neutrophil differentiation from pre-neutrophils to immature neutrophils. Using the progenitor cell line, we also confirmed that Cepbe is required for neutrophil differentiation in vivo, validating the utility of this cell line both for screening and for studying in vivo phenotypes. The genome-wide screen also identified all components of the WASH complex as being required for neutrophil differentiation, a finding that extends the known role of WASH in hematopoietic stem cell differentiation to later stages of neutrophil development. Taken together, we demonstrate that Cas9+ER-Hoxb8 immortalized neutrophils can be used to study neutrophil function both in vitro and in vivo. This new resource will enable the analysis of the role of neutrophils in numerous disease states using genetics for the first time.

immunology↗

bioRxiv2022

Integrated analysis of Wnt signalling system component gene expression

Wnt signalling controls patterning and differentiation across many tissues and organs of the developing embryo via temporally and spatially restricted expression of multi-gene families encoding ligands, receptors, pathway modulators and intracellular components. Here we report an integrated analysis of key encoding genes in the 3D space of the mouse embryo across multiple stages of development. We applied a method for 3D/3D image transformation to map all gene expression patterns to a single reference embryo for each stage providing both visual analysis and volumetric mapping allowing computational methods to interrogate the combined expression patterns. We identify novel territories where multiple Wnt and Fzd genes are co-expressed and cross-compare all patterns, including all seven Wnt paralogous gene pairs. The comprehensive analysis allows regions in the embryo where no Wnt or Fzd gene expression is detected, and where single Wnt genes are uniquely expressed, to be revealed. This work provides insight into a level of organisation of the patterns not previously possible, as well as presenting a resource that can be utilised further by the research community for whole system analysis.

developmental biology↗

bioRxiv2022

WlzWarp: An Open-Source Tool for Complex Alignment of Spatial Data

BackgroundThe spatio-temporal organisation of many biological processes such as gene-expression and neuronal activity is critical to understanding the overall biological behaviour, phenotype and disease. This is especially true during embryonic development. During development spatial patterns of gene expression are key to segmentation, tissue differentiation and organ development. In situ techniques can reveal the activity of genes and the presence of proteins to a very high sub-cellular resolution but typically at high resolution only a few probes can be used on any sample therefore to compare many such patterns requires mapping of image-based data to a standard spatial framework. Once mapped those data can be collated, queried and analysed in purely spatial terms to reveal unknown combinatorial gene-activity that could not be discovered any other way. Mapping spatial data to image domains with systematic variation in shape and pose, such as embryos or elongated organs, presents special problems. Automated techniques available for more constrained systems can not deliver the mapping fidelity required to analyse these data therefore we have developed a manual editing tool, WlzWarp, for mapping 3D image data using the constrained distance transform (CDT) which uniquely can deliver the complex transforms required. ResultsWe have implemented a fully open-source tool (available on GitHub), WlzWarp to provide interactive complex spatial mapping of 3D image data. We have applied WlzWarp to map a set of gene-expression patterns in the developing mouse embryo that could not be mapped by any other technique. The transform procedure was tested by using multiple images of the same gene from independent samples and thereby testing the full end-to-end mapping process. WlzWarp is implemented in C++ using open-source packages Qt, Coin and SIMVoleon for cross-architecture compatibility. It has been developed under Linux but also tested on Mac OSX and MS Windows. ConclusionsWlzWarp is a freely available software tool for non-linear registration and alignment of complex 2D & 3D spatial patterns from one image to another or to an atlas model. It has been tested in the context of embryo data but can be used for any 3D or 2D image registration problem.

bioinformatics↗

bioRxiv2020

Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy

Mendelian Randomization (MR) exploits genetic variants as instrumental variables to estimate the causal effect of an "exposure" trait on an "outcome" trait from observational data. However, the validity of such studies is threatened by population stratification, batch effects, and horizontal pleiotropy. Although a variety of methods have been proposed to partially mitigate those problems, residual biases may still remain, leading to highly statistically significant false positives in large genetic databases. Here, we describe a suite of sensitivity analysis tools for MR that enables investigators to properly quantify the robustness of their findings against these (and other) unobserved validity threats. Specifically, we propose the routine reporting of sensitivity statistics that can be used to readily quantify the robustness of a MR result: (i) the partial R2 of the genetic instrument with the exposure and the outcome traits; and, (ii) the robustness value of both genetic associations. These statistics quantify the minimal strength of violations of the MR assumptions that would be necessary to explain away the MR causal effect estimate. We also provide intuitive displays to visualize the sensitivity of the MR estimate to any degree of violation, and formal methods to bound the worst-case bias caused by violations in terms of multiples of the observed strength of principal components, batch effects, as well as putative pleiotropic pathways. We demonstrate how these tools can aid researchers in distinguishing robust from fragile findings, by showing that the MR estimate of the causal effect of body mass index (BMI) on diastolic blood pressure is relatively robust, whereas the MR estimate of the causal effect of BMI on Townsend deprivation index is relatively fragile.

genetics↗

bioRxiv2020

Chromatin-associated effectors of energy-sensing pathways mediate intergenerational effects

Environmental stimuli experienced by the parental generation influence the phenotype of subsequent generations. The effects of these stimuli on the parental generation may be passed through the germline, but the mechanisms of this non-Mendelian type of inheritance are poorly known. Here we show that modulation of nutrient-sensing pathways in the parental generation of a nematode (Auanema freiburgensis) regulates phenotypic plasticity of its offspring. In response to pheromones, AMP-activated protein kinase (AMPK), mechanistic target of rapamycin complex 1 (mTORC1) and insulin signaling regulate stress resistance and sex determination across a generation. The effectors of these pathways are closely associated with the chromatin and their regulation affects the acetylation chromatin status in the germline. These results suggest that highly conserved metabolic sensors regulate phenotypic plasticity by changing the epigenetic status of the germline.

developmental biology↗

bioRxiv2020

Spatial Transcriptional Mapping of the Human Nephrogenic Program

Congenital abnormalities of the kidney and urinary tract are amongst the most common birth defects affecting 3% of newborns. The human kidney develops over a 30-week period in which a nephron progenitor pool gives rise to around a million nephrons. To establish a framework for human nephrogenesis, we spatially resolved a stereotypical process by which equipotent nephron progenitors generate a nephron anlagen, then applied data-driven approaches to construct three-dimensional protein maps on anatomical models of the nephrogenic program. Single cell RNA sequencing identified novel progenitor states which were spatially mapped to the nephron anatomy enabling the generation of functional gene-networks predicting interactions within and between nephron cell-types. Network mining identified known developmental disease genes and predicts new targets of interest. The spatially resolved nephrogenic program made available through the Human Nephrogenesis Atlas (https://sckidney.flatironinstitute.org/) will facilitate an understanding of kidney development and disease, and enhance efforts to generate new kidney structures.

cell biology↗

bioRxiv2020

BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching

Single-cell RNA-Sequencing (scRNA-Seq) is a set of technologies used to profile gene expression at the level of individual cells. Although the throughput of scRNA-Seq experiments is steadily growing in terms of the number of cells, large datasets are not yet commonly used due to prohibitively high costs. Integrating multiple datasets into one can improve power in scRNA-Seq experiments, and efficient integration is very important for downstream analyses such as identifying cell-type-specific eQTLs. State-of-the-art scRNA-Seq integration methods are based on the mutual nearest neighbors paradigm and fail to both correct for batch effects and maintain the local structure of the datasets. In this paper, we propose a novel scRNA-Seq dataset integration method called BATMAN (BATch integration via minimum-weight MAtchiNg). Across multiple simulations and real datasets, we show that our method significantly outperforms state-of-the-art tools with respect to existing metrics for batch effects by up to 80% while retaining cell-to-cell relationships. BATMAN is available at https://github.com/mandricigor/batman.

bioinformatics↗