The abundance of new computational methods for processing and interpreting transcriptomes at a single cell level raises the need for in silico platforms for evaluation and validation. Here, we ...present SymSim, a simulator that explicitly models the processes that give rise to data observed in single cell RNA-Seq experiments. The components of the SymSim pipeline pertain to the three primary sources of variation in single cell RNA-Seq data: noise intrinsic to the process of transcription, extrinsic variation indicative of different cell states (both discrete and continuous), and technical variation due to low sensitivity and measurement noise and bias. We demonstrate how SymSim can be used for benchmarking methods for clustering, differential expression and trajectory inference, and for examining the effects of various parameters on their performance. We also show how SymSim can be used to evaluate the number of cells required to detect a rare population under various scenarios.
Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understanding of CSF leukocytes remains superficial. Here, using ...single cell transcriptomics, we identify a specific location-associated composition and transcriptome of CSF leukocytes. Multiple sclerosis (MS) - an autoimmune disease of the CNS - increases transcriptional diversity in blood, but increases cell type diversity in CSF including a higher abundance of cytotoxic phenotype T helper cells. An analytical approach, named cell set enrichment analysis (CSEA) identifies a cluster-independent increase of follicular (TFH) cells potentially driving the known expansion of B lineage cells in the CSF in MS. In mice, TFH cells accordingly promote B cell infiltration into the CNS and the severity of MS animal models. Immune mechanisms in MS are thus highly compartmentalized and indicate ongoing local T/B cell interaction.
As the number of single‐cell transcriptomics datasets grows, the natural next step is to integrate the accumulating data to achieve a common ontology of cell types and states. However, it is not ...straightforward to compare gene expression levels across datasets and to automatically assign cell type labels in a new dataset based on existing annotations. In this manuscript, we demonstrate that our previously developed method, scVI, provides an effective and fully probabilistic approach for joint representation and analysis of scRNA‐seq data, while accounting for uncertainty caused by biological and measurement noise. We also introduce single‐cell ANnotation using Variational Inference (scANVI), a semi‐supervised variant of scVI designed to leverage existing cell state annotations. We demonstrate that scVI and scANVI compare favorably to state‐of‐the‐art methods for data integration and cell state annotation in terms of accuracy, scalability, and adaptability to challenging settings. In contrast to existing methods, scVI and scANVI integrate multiple datasets with a single generative model that can be directly used for downstream tasks, such as differential expression. Both methods are easily accessible through scvi‐tools.
SYNOPSIS
This study demonstrates the ability of scVI to integrate single‐cell RNA‐seq datasets in a variety of settings and presents scANVI, a new development based on scVI for automated annotation of cell types and states.
In scVI, datasets from different labs and technologies are integrated in a joint latent space.
In scANVI, cell type annotations are transferred between datasets and across different scenarios.
Uncertainties of differential gene expression in multiple samples are quantified.
The performance of scVI and scANVI in data integration and cell state annotation is superior to other related methods.
This study demonstrates the ability of scVI to integrate single‐cell RNA‐seq datasets in a variety of settings and presents scANVI, a new development based on scVI for automated annotation of cell types and states.
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale ...genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.
Macrophages are the main target cells for
Mycobacterium tuberculosis
(Mtb) infection. Previous studies have shown that Mtb actively upregulates phosphorus transport proteins, such as Rv0928 protein ...(also known as PstS3), to increase inorganic phosphate uptake and promote their survival under low phosphorus culture conditions
in vitro
. However, it is unclear whether this upregulation of PstS3 affects the intracellular survival of Mtb, as the latter is also largely dependent on the immune response of infected macrophages. By using Rv0928-overexpressing
Mycobacterium smegmatis
(Ms::Rv0928), we unexpectedly found that Rv0928 not only increased apoptosis, but also augmented the inflammatory response of infected macrophages. These enhanced cellular defense mechanisms ultimately led to a dramatic reduction in intracellular bacterial load. By investigating the underlying mechanisms, we found that Rv0928 interacted with the macrophage mitochondrial phosphate carrier protein SLC25A3, reduced mitochondrial membrane potential and caused mitochondrial cytochrome c release, which ultimately activated caspase-9-mediated intrinsic apoptosis. In addition, Rv0928 amplified macrophage mitochondrial ROS production, further enhancing pro-inflammatory cytokine production by promoting activation of NF-κB and MAPK pathways. Our study suggested that Mtb Rv0928 up-regulation enhanced the immune defense response of macrophages. These findings may help us to better understand the complex process of mutual adaptation and mutual regulation between Mtb and macrophages during infection.
The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays ...has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia.
Conventional dendritic cells (cDCs), cDC1 and cDC2, act both to initiate immunity and maintain self-tolerance. The tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) is used by cDCs in ...maintaining tolerance, but its role in different subsets remains unclear. At homeostasis, only mature CCR7+ cDC1 expressed IDO1 that was dependent on IRF8. Lipopolysaccharide treatment induced maturation and IDO1-dependent tolerogenic activity in isolated immature cDC1, but not isolated cDC2. However, both human and mouse cDC2 could induce IDO1 and acquire tolerogenic function when co-cultured with mature cDC1 through the action of cDC1-derived l-kynurenine. Accordingly, cDC1-specific inactivation of IDO1 in vivo exacerbated disease in experimental autoimmune encephalomyelitis. This study identifies a previously unrecognized metabolic communication in which IDO1-expressing cDC1 cells extend their immunoregulatory capacity to the cDC2 subset through their production of tryptophan metabolite l-kynurenine. This metabolic axis represents a potential therapeutic target in treating autoimmune demyelinating diseases.
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•The tolerogenic IDO1 pathway is expressed in mature cDC1 but not in cDC2•Mature IDO1+ cDC1 are regulatory in vitro and in vivo•IDO1 competent cDC1 induce regulatory cDC2 via Trp metabolism•l-kynurenine recruits AhR competent cDC2 into a tolerogenic pool
Activation of the tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) induces DC tolerance, but how this pathway is used by selected cDC subsets is currently unclear. Gargaro et al. show that activation of the IDO1 pathway, which is expressed in mature cDC1 but not in cDC2, induces regulatory cDC2 via AhR-mediated metabolic communication.
Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to ...study both human history and adaptation. The amount and quality of ancient human data continue to improve and enable tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred and to revise previous conjectures. In this article, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a case in point, we focus on one of the most celebrated examples of human adaptation: the evolution of lactase persistence. We briefly review this dietary adaptation and argue that, effectively, the evolutionary history of lactase persistence is still not fully resolved. We propose that, by leveraging data from multiple populations across time and space, we will find evidence of a more nuanced history than just a simple selective sweep. We support our hypotheses with simulation results and make some cautionary notes regarding the use of haplotype-based summary statistics to estimate evolutionary parameters.
Epilepsy is not only a chronic neurological disorder but also a condition associated with other comorbidities. The purpose of this study was to determine the prevalence of major depression in a ...cohort of adult patients with epilepsy (PWEs) living in north China, and investigate the predictors of major depression in PWEs. A total of 215 consecutive cases were enrolled and divided into two groups: PWEs with major depression and PWEs without major depression. Patients were assessed for demographic characteristics, epilepsy details, and social status. A total of 65 of 215 (30.23%) PWEs exhibited comorbid major depression. A binary logistic regression model revealed the strong predictor variables of major depression to be drug responsiveness (odds ratio OR=0.23; p=0<0.01; 95% CI 0.13-0.39), presence of chronic medical illnesses (OR=0.19; p=0.015<0.05; 95% CI 0.05-0.72), and employment status (OR=0.42; p=0.015<0.05; 95% CI 0.21-0.84).
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