The majority of common risk alleles identified for neuropsychiatric disorders reside in noncoding regions of the genome and are therefore likely to impact gene regulation. However, the genes that are ...primarily affected and the nature and developmental timing of these effects remain unclear. Given the hypothesized role for early neurodevelopmental processes in these conditions, we here define genetic predictors of gene expression in the human fetal brain with which we perform transcriptome-wide association studies (TWASs) of attention deficit hyperactivity disorder (ADHD), autism spectrum disorder, bipolar disorder, major depressive disorder, and schizophrenia. We identify prenatal cis-regulatory effects on 63 genes and 166 individual transcripts associated with genetic risk for these conditions. We observe pleiotropic effects of expression predictors for a number of genes and transcripts, including those of decreased DDHD2 expression in association with risk for schizophrenia and bipolar disorder, increased expression of a ST3GAL3 transcript with risk for schizophrenia and ADHD, and increased expression of an XPNPEP3 transcript with risk for schizophrenia, bipolar disorder, and major depression. For the protocadherin alpha cluster genes PCDHA7 and PCDHA8, we find that predictors of low expression are associated with risk for major depressive disorder while those of higher expression are associated with risk for schizophrenia. Our findings support a role for altered gene regulation in the prenatal brain in susceptibility to various neuropsychiatric disorders and prioritize potential risk genes for further neurobiological investigation.
Glycogen, a branched glucose polymer, helps regulate glucose homeostasis through immediate storage and release of glucose. Reprogramming of glycogen metabolism has recently been suggested to play an ...emerging role in cancer progression and tumorigenesis. However, regulation of metabolic rewiring for glycogen synthesis and breakdown in cancer cells remains less understood. Despite the availability of various glycogen detection methods, selective visualization of glycogen in living cells with high spatial resolution has proven to be highly challenging. Here, we present an optical imaging strategy to visualize glycogen in live cancer cells with minimal perturbation by combining stimulated Raman scattering microscopy with metabolic incorporation of deuterium-labeled glucose. We revealed the subcellular enrichment of glycogen in live cancer cells and achieved specific glycogen mapping through distinct spectral identification. Using this method, different glycogen metabolic phenotypes were characterized in a series of patient-derived BRAF mutant melanoma cell lines. Our results indicate that cell lines manifesting high glycogen storage level showed increased tolerance to glucose deficiency among the studied melanoma phenotypes. This method opens up the possibility for noninvasive study of complex glycogen metabolism at subcellular resolution and may help reveal new features of glycogen regulation in cancer systems.
During the past 15 years or so, nanowires (NWs) have emerged as a new and distinct class of materials. Their novel structural and physical properties separate them from wires that can be prepared ...using the standard methods for manufacturing electronics. NW-based applications that range from traditional electronic devices (logic and memory) to novel biomolecular and chemical sensors, thermoelectric materials, and optoelectronic devices, all have appeared during the past few years. From a fundamental perspective, NWs provide a route toward the investigation of new physics in confined dimensions. Perhaps the most familiar fabrication method is the vapor−liquid−solid (VLS) growth technique, which produces semiconductor nanowires as bulk materials. However, other fabrication methods exist and have their own advantages. In this Account, I review a particular class of NWs produced by an alternative method called superlattice nanowire pattern transfer (SNAP). The SNAP method is distinct from other nanowire preparation methods in several ways. It can produce large NW arrays from virtually any thin-film material, including metals, insulators, and semiconductors. The dimensions of the NWs can be controlled with near-atomic precision, and NW widths and spacings can be as small as a few nanometers. In addition, SNAP is almost fully compatible with more traditional methods for manufacturing electronics. The motivation behind the development of SNAP was to have a general nanofabrication method for preparing electronics-grade circuitry, but one that would operate at macromolecular dimensions and with access to a broad materials set. Thus, electronics applications, including novel demultiplexing architectures; large-scale, ultrahigh-density memory circuits; and complementary symmetry nanowire logic circuits, have served as drivers for developing various aspects of the SNAP method. Some of that work is reviewed here. As the SNAP method has evolved into a robust nanofabrication method, it has become an enabling tool for the investigation of new physics. In particular, the application of SNAP toward understanding heat transport in low-dimensional systems is discussed. This work has led to the surprising discovery that Si NWs can serve as highly efficient thermoelectric materials. Finally, we turn toward the application of SNAP to the investigation of quasi-one-dimensional (quasi-1D) superconducting physics in extremely high aspect ratio Nb NWs.
Chiral amine diastereomers are ubiquitous in pharmaceuticals and agrochemicals
, yet their preparation often relies on low-efficiency multi-step synthesis
. These valuable compounds must be ...manufactured asymmetrically, as their biochemical properties can differ based on the chirality of the molecule. Herein we characterize a multifunctional biocatalyst for amine synthesis, which operates using a mechanism that is, to our knowledge, previously unreported. This enzyme (EneIRED), identified within a metagenomic imine reductase (IRED) collection
and originating from an unclassified Pseudomonas species, possesses an unusual active site architecture that facilitates amine-activated conjugate alkene reduction followed by reductive amination. This enzyme can couple a broad selection of α,β-unsaturated carbonyls with amines for the efficient preparation of chiral amine diastereomers bearing up to three stereocentres. Mechanistic and structural studies have been carried out to delineate the order of individual steps catalysed by EneIRED, which have led to a proposal for the overall catalytic cycle. This work shows that the IRED family can serve as a platform for facilitating the discovery of further enzymatic activities for application in synthetic biology and organic synthesis.
We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws ...collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.
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•Analysis of serial blood from 139 COVID-19 patients reveals immune coordination•A major immunological shift is seen between mild and moderate infection•Moderate and severe cases exhibit inflammation and a sharp drop in blood nutrients•Novel immune cell subsets emerge in moderate cases and increase with severity
Using serial blood draws from COVID-19 patients, Su et al. present an extensive multi-omics dataset of plasma and single PBMCs covering the first week of infection following clinical diagnosis, which includes information on plasma proteins, metabolites, and on PBMC transcriptomic and surface-protein data, immune receptor sequences, secreted proteins, and electronic health record data. Their integrated analysis identifies a major immunological shift between mild and moderate infection, which includes an increase in inflammation, drop in blood nutrients, and the emergence of novel immune cell subpopulations that intensify with disease severity.
Phenotypic plasticity is associated with non-genetic drug tolerance in several cancers. Such plasticity can arise from chromatin remodeling, transcriptomic reprogramming, and/or protein signaling ...rewiring, and is characterized as a cell state transition in response to molecular or physical perturbations. This, in turn, can confound interpretations of drug responses and resistance development. Using BRAF-mutant melanoma cell lines as the prototype, we report on a joint theoretical and experimental investigation of the cell-state transition dynamics associated with BRAF inhibitor drug tolerance. Thermodynamically motivated surprisal analysis of transcriptome data was used to treat the cell population as an entropy maximizing system under the influence of time-dependent constraints. This permits the extraction of an epigenetic potential landscape for drug-induced phenotypic evolution. Single-cell flow cytometry data of the same system were modeled with a modified Fokker-Planck-type kinetic model. The two approaches yield a consistent picture that accounts for the phenotypic heterogeneity observed over the course of drug tolerance development. The results reveal that, in certain plastic cancers, the population heterogeneity and evolution of cell phenotypes may be understood by accounting for the competing interactions of the epigenetic potential landscape and state-dependent cell proliferation. Accounting for such competition permits accurate, experimentally verifiable predictions that can potentially guide the design of effective treatment strategies.
Antigen-specific CD8+ T cells mediate pathogen clearance. T cell phenotype is influenced by T cell receptor (TCR) sequences and environmental signals. Quantitative comparisons of these factors in ...human disease, while challenging to obtain, can provide foundational insights into basic T cell biology. Here, we investigate the phenotype kinetics of 679 CD8+ T cell clonotypes, each with specificity against one of three immunogenic viral antigens. Data were collected from a longitudinal study of 68 COVID-19 patients with antigens from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cytomegalovirus (CMV), and influenza. Each antigen is associated with a different type of immune activation during COVID-19. We find TCR sequence to be by far the most important factor in shaping T cell phenotype and persistence for populations specific to any of these antigens. Our work demonstrates the important relationship between TCR sequence and T cell phenotype and persistence and helps explain why T cell phenotype often appears to be determined early in an infection.
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•TCR sequence similarity correlates with CD8+ T cell phenotype similarity•Antigen-specific CD8+ T cell behavior and persistence associates with TCR sequence•TCR sequences have a greater impact than environmental signals on phenotype•Even bystander T cell phenotype is most affected by TCR sequence, not environment
Chen et al. demonstrate that for immunogenic viral antigens, in both active infection and bystander activation contexts, TCR sequences are quantitatively the most important factor for antigen-specific CD8+ T cell phenotype and out-compete environmental signals such as plasma cytokines in terms of phenotypic impact.
The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge for understanding biological changes ranging from cellular differentiation to ...epigenetic responses of diseased cells upon drugging. We integrate experiments and theory to determine the trajectories that single BRAF
mutant melanoma cancer cells take between drug-naive and drug-tolerant states. Although single-cell omics tools can yield snapshots of the cell-state landscape, the determination of individual cell trajectories through that space can be confounded by stochastic cell-state switching. We assayed for a panel of signaling, phenotypic, and metabolic regulators at points across 5 days of drug treatment to uncover a cell-state landscape with two paths connecting drug-naive and drug-tolerant states. The trajectory a given cell takes depends upon the drug-naive level of a lineage-restricted transcription factor. Each trajectory exhibits unique druggable susceptibilities, thus updating the paradigm of adaptive resistance development in an isogenic cell population.
Continuous BRAF inhibition of BRAF mutant melanomas triggers a series of cell state changes that lead to therapy resistance and escape from immune control before establishing acquired resistance ...genetically. We used genome-wide transcriptomics and single-cell phenotyping to explore the response kinetics to BRAF inhibition for a panel of patient-derived BRAFV600
-mutant melanoma cell lines. A subset of plastic cell lines, which followed a trajectory covering multiple known cell state transitions, provided models for more detailed biophysical investigations. Markov modeling revealed that the cell state transitions were reversible and mediated by both Lamarckian induction and nongenetic Darwinian selection of drug-tolerant states. Single-cell functional proteomics revealed activation of certain signaling networks shortly after BRAF inhibition, and before the appearance of drug-resistant phenotypes. Drug targeting those networks, in combination with BRAF inhibition, halted the adaptive transition and led to prolonged growth inhibition in multiple patient-derived cell lines.
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