Paul Francis Harrison

The emergence of Candida auris as a pathogen required host adaptation and evasion of mammalian immunity, but the mechanisms are poorly understood. We discovered that C. auris uses nutrient sensing to tune its virulence traits and modulate immune activation in changing environments. In glucose-rich conditions (relevant to blood), C. auris suppresses its virulence traits and evades immune detection. Conversely, non-fermentable carbon sources prevalent in skin activate adhesion and filamentation, thereby triggering macrophage responses. Activation of adhesion by non-fermentable carbon sources is recapitulated across diverse C. auris strains, while filamentation is heterogeneous. In-depth phenotyping of multiple clinical strains revealed that C. auris generates phenotypic heterogeneity by titrating expression of key transcriptional regulators dependent on nutrient inputs and genetic background. This modulates its virulence potential and controls proportional immune responses. Therefore, metabolic flexibility enables C. auris to optimize a critical trade-off: expressing virulence traits while minimizing immune recognition to colonize host tissues.

The emergence of Candida auris as a pathogen required host adaptation and evasion of mammalian immunity, but the mechanisms are poorly understood. We discovered that C. auris uses nutrient sensing to tune its virulence potential and control immune activation in changing environments. In glucose-rich conditions (relevant to blood), C. auris suppresses its virulence traits and evades immune detection. Conversely, carbon sources prevalent in skin activate adhesion and filamentation, thereby triggering robust macrophage responses. In-depth phenotyping of multiple clinical strains revealed that C. auris generates phenotypic heterogeneity by titrating expression of key transcriptional regulators dependent on nutrient inputs and genetic background. This dials-up or -down its virulence potential and controls proportional immune responses and host colonisation. Therefore, metabolic flexibility enables C. auris to optimise a critical trade-off: expressing traits for tissue colonization while minimizing immune recognition. This establishes how C. auris adjusts its virulence and immune evasion to thrive in host environments.

Simulated high-dimensional data is useful for testing, validating, and improving algorithms used in dimension reduction, supervised and unsupervised learning. High-dimensional data is characterized by multiple variables that are dependent or associated in some way, such as linear, nonlinear, clustering or anomalies. Here we provide new methods for generating a variety of high-dimensional structures using mathematical functions and statistical distributions organized into the R package cardinalR. Several example data sets are also provided. These will be useful for researchers to better understand how different analytical methods work and can be improved, with a special focus on nonlinear dimension reduction methods. This package enriches the existing toolset of benchmark datasets for evaluating algorithms.

Nonlinear dimension reduction methods provide a low-dimensional representation of high-dimensional data by applying a Nonlinear transformation. However, the complexity of the transformations and data structures can create wildly different representations depending on the method and hyper-parameter choices. It is difficult to determine whether any of these representations are accurate, which one is the best, or whether they have missed important structures. The R package quollr has been developed as a new visual tool to determine which method and which hyper-parameter choices provide the most accurate representation of high-dimensional data. The scurve data from the package is used to illustrate the algorithm. Single-cell RNA sequencing (scRNA-seq) data from mouse limb muscles are used to demonstrate the usability of the package.

ADAR1 edits adenosine to inosine (A-to-I) in double-stranded RNA to prevent MDA5 sensing of cellular transcripts, its key physiological role. However, editing-independent functions of ADAR1 remain poorly understood. Using a series of Adar1 mutant mice rescued by loss of MDA5 and PKR, we investigated isoform-specific, editing-independent roles of ADAR1 in vivo . We found that the cytoplasmic ADAR1p150 isoform is essential for maintaining peripheral T cell numbers and differentiation of hematopoietic stem and progenitor cells (HSPCs). In bone marrow transplants, ADAR1p150 protein, but not its editing activity, was crucial for T cell regeneration and HSPC repopulation, demonstrating a cell-intrinsic function in hematopoiesis. Experiments with IFNβ-treatment of purified HSPCs in vitro and in vivo IFNAR1 neutralization revealed hypersensitivity to tonic type I interferon (IFN) in the absence of ADAR1p150. Using cell lines, we demonstrate that type I IFN activates the OAS-RNaseL pathway, leading to cell death. This study shows that tonic type I IFN induces immunogenic cellular RNAs in sterile conditions. ADAR1p150 suppresses immune sensing of self-dsRNAs through both editing-dependent (MDA5) and editing-independent (PKR, OAS-RNaseL) mechanisms. Thus, ADAR1p150 protein levels and activity combine to set the threshold for tolerance to self-derived dsRNAs.

Alternative polyadenylation has been linked to multiple developmental and disease transitions. The prevailing hypothesis being that differentiated cells use longer 3’ UTRs with expended regulatory capacity whereas undifferentiated cells use shorter 3’ UTRs. Here, we describe the gene expression and alternative polyadenylation profiles of human primary myoblasts over a time course of differentiation. Contrary to expectations, only minor changes in the 3’ end choice were observed. To reconcile this finding with published research, we devised a new bioinformatic method to compare the degree of alternative polyadenylation in the differentiation of primary human and immortalized murine (C ₂ C ₁₂ ) myoblasts. Differentiated human primary myotubes display only half the alternative polyadenylation of the mouse model, with less than 1/10 of the genes undergoing alternative polyadenylation in C ₂ C ₁₂ cells showing evidence of alternative processing in human primary muscle differentiation. A global reduction in the expression of cleavage and polyadenylation factors in C ₂ C ₁₂ , but not in primary human myotubes may explain the lack of alternative polyadenylation in this system. Looking more broadly at transcriptome changes across differentiation shows that less than half of the genes differentially expressed in the immortalized model were recapitulated in primary cells. Of these, important metabolic pathways, such as glycolysis and sterol biosynthesis, showed divergent regulation. Collectively, our data caution against using immortalized cell lines, which may not fully recapitulate human muscle development, and suggest that alternative polyadenylation in the differentiation of primary cells might be less pronounced than previously thought.

SUMMARY: The differentiation of naïve CD8 ⁺ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8 ⁺ T cells. We observed that the architecture of the naive CD8 ⁺ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8 ⁺ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state. One Sentence Summary: CD8 ⁺ T cell naïvety is actively maintained by transcription factors that enforce a distinct, naïve chromatin architecture. Highlights: CD8 ⁺ T cell differentiation states are underscored by distinct chromatin looping architectures. Chromatin loops juxtapose CTL state appropriate enhancers, transcription factors and genes. Effector and memory CTLs have similar genome architectures, explaining rapid memory recall. CTL differentiation is restrained by BACH2 and SATB1, which enforce a naïve loop architecture.

Langevitour displays interactive animated 2D projections of high-dimensional datasets. Langevin Dynamics is used to produce a smooth path of projections. Projections are initially explored at random. A “guide” can be activated to look for an informative projection, or variables can be manually positioned. After a projection of particular interest has been found, continuing small motions provide a channel of visual information not present in a static scatter-plot. langevitour is implemented in Javascript, allowing for a high frame rate and responsive interaction, and can be used directly from the R environment or embedded in HTML documents produced using R. The widget is demonstrated using single-cell RNA sequencing (scRNA-Seq) data. langevitour’s linear projections provide a less distorted view of this data than commonly used non-linear dimensionality reductions such as UMAP.