Nat Commun. 2023 Oct 12;14(1):6414. doi: 10.1038/s41467-023-42101-z.

ABSTRACT

Myelofibrosis is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. Myelofibrosis patients frequently carry driver mutations in either JAK2 or Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across myelofibrosis patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three targetable vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high endoplasmic reticulum (ER) stress, responding to ER stressors and unfolded protein response inhibition. Overall, our integrated analyses provide a molecularly motivated roadmap for individualized myelofibrosis patient treatment.

PMID:37828014 | DOI:10.1038/s41467-023-42101-z

Nat Commun. 2023 Oct 12;14(1):6417. doi: 10.1038/s41467-023-42144-2.

ABSTRACT

Despite their fundamental role in resolving viral infections, our understanding of how polyclonal neutralizing antibody responses target non-enveloped viruses remains limited. To define these responses, we obtained the full antigenic profile of multiple human and mouse polyclonal sera targeting the capsid of a prototypical picornavirus, coxsackievirus B3. Our results uncover significant variation in the breadth and strength of neutralization sites targeted by individual human polyclonal responses, which contrasted with homogenous responses observed in experimentally infected mice. We further use these comprehensive antigenic profiles to define key structural and evolutionary parameters that are predictive of escape, assess epitope dominance at the population level, and reveal a need for at least two mutations to achieve significant escape from multiple sera. Overall, our data provide a comprehensive analysis of how polyclonal sera target a non-enveloped viral capsid and help define both immune dominance and escape at the population level.

PMID:37828013 | DOI:10.1038/s41467-023-42144-2

ACS Nano. 2023 Oct 12. doi: 10.1021/acsnano.3c08034. Online ahead of print.

ABSTRACT

Tumor-associated macrophages (TAM) interact with cancer and stromal cells and are integral to sustaining many cancer-promoting features. Therapeutic manipulation of TAM could therefore improve clinical outcomes and synergize with immunotherapy and other cancer therapies. While different nanocarriers have been used to target TAM, a knowledge gap exists on which TAM pathways to target and what payloads to deliver for optimal antitumor effects. We hypothesized that a multipart combination involving the Janus tyrosine kinase (JAK), noncanonical nuclear factor kappa light chain enhancer of activated B cells (NF-κB), and toll-like receptor (TLR) pathways could lead to a highly active myeloid therapy (HAMT). Thus, we devised a screen to determine drug combinations that yield maximum IL-12 production from myeloid cells to treat the otherwise highly immunosuppressive myeloid environments in tumors. Here we show the extraordinary efficacy of a triple small-molecule combination in a TAM-targeted nanoparticle for eradicating murine tumors, jumpstarting a highly efficient antitumor response by adopting a distinctive antitumor TAM phenotype and synergizing with other immunotherapies. The HAMT therapy represents a recently developed approach in immunotherapy and leads to durable responses in murine cancer models.

PMID:37824733 | DOI:10.1021/acsnano.3c08034

Science. 2023 Oct 13;382(6667):eadf5357. doi: 10.1126/science.adf5357. Epub 2023 Oct 13.

ABSTRACT

Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.

PMID:37824674 | DOI:10.1126/science.adf5357

PLoS One. 2023 Oct 12;18(10):e0292585. doi: 10.1371/journal.pone.0292585. eCollection 2023.

ABSTRACT

Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of the fruit fly Drosophila melanogaster. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growth. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would facilitate the identification of the molecular mechanisms for the metabolic interactions between them. While numerous CDMs have been developed that support specific strains of lactobacilli or Acetobacter, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous CDM designed for growth of lactobacilli, by modifying the nutrient abundances to improve growth yield. We further simplified the medium by substituting casamino acids in place of individual amino acids and the standard Wolfe's vitamins and mineral stocks in place of individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. These stock solutions can be used to prepare several CDM formulations that support robust growth of numerous lactobacilli and Acetobacters. Here, we provide the composition and several examples of its use, which is important for tractability in dissecting the genetic and metabolic basis of natural bacterial species interactions.

PMID:37824485 | DOI:10.1371/journal.pone.0292585

Microbiol Spectr. 2023 Oct 12:e0266323. doi: 10.1128/spectrum.02663-23. Online ahead of print.

ABSTRACT

High-throughput sequencing (HTS) is an important tool for plant virus detection and discovery. HTS technologies such as Nanopore sequencing has been rapidly developing in recent years, and offers new possibilities for fast routine diagnostic applications. This study compared MiSeq (Illumina) RNA-Seq with the MinION sequencer (Oxford Nanopore Technologies) (ONT) direct-RNA-Seq methods to detect and sequence the broad bean wilt virus 2 (BBWV2) genome. The Illumina BBWV2 RNA1 and RNA2 genome segments were intact and matched with ONT with 99.1% and 98.8% nucleotide identity (nt) match, respectively. The RNA1 genome derived from ONT had deletions within the nucleoside-triphosphate binding and protease factor open-reading frames, and the upstream of five untranslated regions. However, its RNA2 was intact, and no sequencing errors were observed. The ONT and Illumina RNA1 and RNA 2 BBWV2 genome segments clustered together phylogenetically along with other none-Fabaceae species, BBWV2 RNA1 NCBI accession KC790225, and RNA 2 MW556592 both from China. This is the first BBWV2 genome study reported in Australia and forms part of the strategy to integrate versatile diagnostic genomics tools at the border to safeguard the Australian grains industry. IMPORTANCE Globally, viral diseases impair the growth and vigor of cultivated crops such as grains, leading to a significant reduction in quality, marketability, and competitiveness. As an island nation, Australia has a distinct advantage in using its border to prevent the introduction of damaging viruses, which threaten the continental agricultural sector. However, breeding programs in Australia rely on imported seeds as new sources of genetic diversity. As such, it is critical to remain vigilant in identifying new and emerging viral pathogens, by ensuring the availability of accurate genomic diagnostic tools at the grain biosecurity border. High-throughput sequencing offers game-changing opportunities in biosecurity routine testing. Genomic results are more accurate and informative compared to traditional molecular methods or biological indexing. The present work contributes to strengthening accurate phytosanitary screening, to safeguard the Australian grains industry, and expedite germplasm release to the end users.

PMID:37823658 | DOI:10.1128/spectrum.02663-23

Cytoskeleton (Hoboken). 2023 Oct 12. doi: 10.1002/cm.21796. Online ahead of print.

ABSTRACT

In January of this year I received an unexpected request from George Bloom to contribute an historical perspective on "the discovery of tau protein," an event that occurred roughly 50 years ago. My first thought was that it could not have been that long ago, as the memories of what was my first independent scientific discovery are still fresh in my mind today. But 50 years is half a century and, as I thought about the events, I realized how much the practice of science has changed.

PMID:37823566 | DOI:10.1002/cm.21796

Elife. 2023 Oct 12;12:e82739. doi: 10.7554/eLife.82739. Online ahead of print.

ABSTRACT

RAF kinase inhibitors can, under certain conditions, increase RAF kinase signaling. This process, which is commonly referred to as 'paradoxical activation' (PA), is incompletely understood. We use mathematical and computational modeling to investigate PA, and we derive rigorous analytical expressions that illuminate the underlying mechanism of this complex phenomenon. We find that conformational autoinhibition modulation by a RAF inhibitor could be sufficient to create PA. We find that experimental RAF-inhibitor drug dose response data that characterize PA across different types of RAF inhibitors are best explained by a model that includes RAF-inhibitor modulation of three properties: conformational autoinhibition, dimer affinity, and drug binding within the dimer (i.e., negative cooperativity). Overall, this work establishes conformational autoinhibition as a robust mechanism for RAF-inhibitor driven PA based solely on equilibrium dynamics of canonical interactions that comprise RAF signaling and inhibition.

PMID:37823369 | DOI:10.7554/eLife.82739

Front Genet. 2023 Sep 26;14:1270185. doi: 10.3389/fgene.2023.1270185. eCollection 2023.

ABSTRACT

Genome-wide association studies (GWAS) involving increasing sample sizes have identified hundreds of genetic variants associated with complex diseases, such as type 2 diabetes (T2D); however, it is unclear how GWAS hits form unique topological structures in protein-protein interaction (PPI) networks. Using persistent homology, this study explores the evolution and persistence of the topological features of T2D GWAS hits in the PPI network with increasing p-value thresholds. We define an n-dimensional persistent disease module as a higher-order generalization of the largest connected component (LCC). The 0-dimensional persistent T2D disease module is the LCC of the T2D GWAS hits, which is significantly detected in the PPI network (196 nodes and 235 edges, P<0.05). In the 1-dimensional homology group analysis, all 18 1-dimensional holes (loops) of the T2D GWAS hits persist over all p-value thresholds. The 1-dimensional persistent T2D disease module comprising these 18 persistent 1-dimensional holes is significantly larger than that expected by chance (59 nodes and 83 edges, P<0.001), indicating a significant topological structure in the PPI network. Our computational topology framework potentially possesses broad applicability to other complex phenotypes in identifying topological features that play an important role in disease pathobiology.

PMID:37823029 | PMC:PMC10562725 | DOI:10.3389/fgene.2023.1270185

Front Bioeng Biotechnol. 2023 Sep 26;11:1297865. doi: 10.3389/fbioe.2023.1297865. eCollection 2023.

NO ABSTRACT

PMID:37823026 | PMC:PMC10562730 | DOI:10.3389/fbioe.2023.1297865

Front Immunol. 2023 Sep 26;14:1254873. doi: 10.3389/fimmu.2023.1254873. eCollection 2023.

ABSTRACT

INTRODUCTION: Severe COVID-19 and non-COVID-19 pulmonary sepsis share pathophysiological, immunological, and clinical features, suggesting that severe COVID-19 is a form of viral sepsis. Our objective was to identify shared gene expression trajectories strongly associated with eventual mortality between severe COVID-19 patients and contemporaneous non-COVID-19 sepsis patients in the intensive care unit (ICU) for potential therapeutic implications.

METHODS: Whole blood was drawn from 20 COVID-19 patients and 22 non-COVID-19 adult sepsis patients at two timepoints: ICU admission and approximately a week later. RNA-Seq was performed on whole blood to identify differentially expressed genes and significantly enriched pathways. Using systems biology methods, drug candidates targeting key genes in the pathophysiology of COVID-19 and sepsis were identified.

RESULTS: When compared to survivors, non-survivors (irrespective of COVID-19 status) had 3.6-fold more "persistent" genes (genes that stayed up/downregulated at both timepoints) (4,289 vs. 1,186 genes); these included persistently downregulated genes in T-cell signaling and persistently upregulated genes in select innate immune and metabolic pathways, indicating unresolved immune dysfunction in non-survivors, while resolution of these processes occurred in survivors. These findings of persistence were further confirmed using two publicly available datasets of COVID-19 and sepsis patients. Systems biology methods identified multiple immunomodulatory drug candidates that could target this persistent immune dysfunction, which could be repurposed for possible therapeutic use in both COVID-19 and sepsis.

DISCUSSION: Transcriptional evidence of persistent immune dysfunction was associated with 28-day mortality in both COVID-19 and non-COVID-19 septic patients. These findings highlight the opportunity for mitigating common mechanisms of immune dysfunction with immunomodulatory therapies for both diseases.

PMID:37822940 | PMC:PMC10562687 | DOI:10.3389/fimmu.2023.1254873

Front Immunol. 2023 Sep 26;14:1257834. doi: 10.3389/fimmu.2023.1257834. eCollection 2023.

ABSTRACT

BACKGROUND: COVID-19 and sepsis represent formidable public health challenges, characterized by incompletely elucidated molecular mechanisms. Elucidating the interplay between COVID-19 and sepsis, particularly in geriatric patients suffering from sepsis-induced acute respiratory distress syndrome (ARDS), is of paramount importance for identifying potential therapeutic interventions to mitigate hospitalization and mortality risks.

METHODS: We employed bioinformatics and systems biology approaches to identify hub genes, shared pathways, molecular biomarkers, and candidate therapeutics for managing sepsis and sepsis-induced ARDS in the context of COVID-19 infection, as well as co-existing or sequentially occurring infections. We corroborated these hub genes utilizing murine sepsis-ARDS models and blood samples derived from geriatric patients afflicted by sepsis-induced ARDS.

RESULTS: Our investigation revealed 189 differentially expressed genes (DEGs) shared among COVID-19 and sepsis datasets. We constructed a protein-protein interaction network, unearthing pivotal hub genes and modules. Notably, nine hub genes displayed significant alterations and correlations with critical inflammatory mediators of pulmonary injury in murine septic lungs. Simultaneously, 12 displayed significant changes and correlations with a neutrophil-recruiting chemokine in geriatric patients with sepsis-induced ARDS. Of these, six hub genes (CD247, CD2, CD40LG, KLRB1, LCN2, RETN) showed significant alterations across COVID-19, sepsis, and geriatric sepsis-induced ARDS. Our single-cell RNA sequencing analysis of hub genes across diverse immune cell types furnished insights into disease pathogenesis. Functional analysis underscored the interconnection between sepsis/sepsis-ARDS and COVID-19, enabling us to pinpoint potential therapeutic targets, transcription factor-gene interactions, DEG-microRNA co-regulatory networks, and prospective drug and chemical compound interactions involving hub genes.

CONCLUSION: Our investigation offers potential therapeutic targets/biomarkers, sheds light on the immune response in geriatric patients with sepsis-induced ARDS, emphasizes the association between sepsis/sepsis-ARDS and COVID-19, and proposes prospective alternative pathways for targeted therapeutic interventions.

PMID:37822934 | PMC:PMC10562607 | DOI:10.3389/fimmu.2023.1257834

PNAS Nexus. 2023 Oct 10;2(10):pgad306. doi: 10.1093/pnasnexus/pgad306. eCollection 2023 Oct.

ABSTRACT

An acidic tumor microenvironment plays a critical role in tumor progression. However, understanding of metabolic reprogramming of tumors in response to acidic extracellular pH has remained elusive. Using comprehensive metabolomic analyses, we demonstrated that acidic extracellular pH (pH 6.8) leads to the accumulation of N1-acetylspermidine, a protumor metabolite, through up-regulation of the expression of spermidine/spermine acetyltransferase 1 (SAT1). Inhibition of SAT1 expression suppressed the accumulation of intra- and extracellular N1-acetylspermidine at acidic pH. Conversely, overexpression of SAT1 increased intra- and extracellular N1-acetylspermidine levels, supporting the proposal that SAT1 is responsible for accumulation of N1-acetylspermidine. While inhibition of SAT1 expression only had a minor effect on cancer cell growth in vitro, SAT1 knockdown significantly decreased tumor growth in vivo, supporting a contribution of the SAT1-N1-acetylspermidine axis to protumor immunity. Immune cell profiling revealed that inhibition of SAT1 expression decreased neutrophil recruitment to the tumor, resulting in impaired angiogenesis and tumor growth. We showed that antineutrophil-neutralizing antibodies suppressed growth in control tumors to a similar extent to that seen in SAT1 knockdown tumors in vivo. Further, a SAT1 signature was found to be correlated with poor patient prognosis. Our findings demonstrate that extracellular acidity stimulates recruitment of protumor neutrophils via the SAT1-N1-acetylspermidine axis, which may represent a metabolic target for antitumor immune therapy.

PMID:37822765 | PMC:PMC10563787 | DOI:10.1093/pnasnexus/pgad306

Front Microbiol. 2023 Sep 26;14:1290062. doi: 10.3389/fmicb.2023.1290062. eCollection 2023.

NO ABSTRACT

PMID:37822741 | PMC:PMC10562684 | DOI:10.3389/fmicb.2023.1290062

Comput Struct Biotechnol J. 2023 Sep 27;21:4729-4742. doi: 10.1016/j.csbj.2023.09.025. eCollection 2023.

ABSTRACT

A clinical incident is typically manifested by several molecular events; therefore, it seems logical that a successful diagnosis, prognosis, or stratification of a clinical landmark require multiple biomarkers. In this report, we presented a machine learning pipeline, namely "Biomarker discovery process at binomial decision point" (2BDP) that took an integrative approach in systematically curating independent variables (e.g., multiple molecular markers) to explain an output variable (e.g., clinical landmark) of binary in nature. In a logical sequence, 2BDP includes feature selection, unsupervised model development and cross validation. In the present work, the efficiency of 2BDP was demonstrated by finding three biomarker panels that independently explained three stages of Alzheimer's disease (AD) marked as Braak stages I, II and III, respectively. We designed three assortments from the entire cohort based on these Braak stages; subsequently, each assortment was split into two populations at Braak score I, II or III. 2BDP systematically integrated random forest and logistic regression fitting model to find biomarker panels with minimum features that explained these three assortments, e.g., significantly differentiated two populations segregated by Braak stage I, II or III, respectively. Thereafter, the efficacies of these panels were measured by the area under the curve (AUC) values of the receiver operating characteristic (ROC) plot. The AUC-ROC was calculated by two cross-validation methods. Final set of gene markers was a mix of novel and a priori established AD signatures. These markers were weighted by unique coefficients and linearly connected in a group of 2-10 to explain Braak stage I, II or III by AUC ≥ 0.8. Small sample size and a lack of distinctly recruited Training and Test sets were the limitations of the present undertaking; yet 2BDP demonstrated its capability to curate a panel of optimum numbers of biomarkers to describe the outcome variable with high efficacy.

PMID:37822559 | PMC:PMC10562676 | DOI:10.1016/j.csbj.2023.09.025

Front Plant Sci. 2023 Sep 26;14:1285875. doi: 10.3389/fpls.2023.1285875. eCollection 2023.

NO ABSTRACT

PMID:37822337 | PMC:PMC10562731 | DOI:10.3389/fpls.2023.1285875

Nature. 2023 Oct 11. doi: 10.1038/s41586-023-06617-0. Online ahead of print.

ABSTRACT

Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses to facilitate vaccine and therapeutic design. However, current strategies for viral evolution prediction are not available early in a pandemic-experimental approaches require host polyclonal antibodies to test against1-16, and existing computational methods draw heavily from current strain prevalence to make reliable predictions of variants of concern17-19. To address this, we developed EVEscape, a generalizable modular framework that combines fitness predictions from a deep learning model of historical sequences with biophysical and structural information. EVEscape quantifies the viral escape potential of mutations at scale and has the advantage of being applicable before surveillance sequencing, experimental scans or three-dimensional structures of antibody complexes are available. We demonstrate that EVEscape, trained on sequences available before 2020, is as accurate as high-throughput experimental scans at anticipating pandemic variation for SARS-CoV-2 and is generalizable to other viruses including influenza, HIV and understudied viruses with pandemic potential such as Lassa and Nipah. We provide continually revised escape scores for all current strains of SARS-CoV-2 and predict probable further mutations to forecast emerging strains as a tool for continuing vaccine development ( evescape.org ).

PMID:37821700 | DOI:10.1038/s41586-023-06617-0

BMJ Open. 2023 Oct 11;13(10):e075332. doi: 10.1136/bmjopen-2023-075332.

ABSTRACT

INTRODUCTION: Obesity is a complex and multifactorial disease that has affected many adolescents in recent decades. Clinical practice guidelines recommend exercise as the key treatment option for adolescents with overweight and obesity. However, the effects of virtual reality (VR) exercise on the physical and brain health of adolescents with overweight and obese remain unclear. This study aims to evaluate the effects of physical and VR exercises on physical and brain outcomes and explore the differences in benefits between them. Moreover, we will apply a multiomics analysis to investigate the mechanism underlying the effects of physical and VR exercises on adolescents with overweight and obesity.

METHODS AND ANALYSIS: This randomised controlled clinical trial will include 220 adolescents with overweight and obesity aged between 11 and 17 years. The participants will be randomised into five groups after screening. Participants in the exercise groups will perform an exercise programme by adding physical or VR table tennis or soccer classes to routine physical education classes in schools three times a week for 8 weeks. Participants in the control group will maintain their usual physical activity. The primary outcome will be the change in body fat mass measured using bioelectrical impedance analysis. The secondary outcomes will include changes in other physical health-related parameters, brain health-related parameters and multiomics variables.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Shanghai Sixth People's Hospital and registered in the Chinese Clinical Trial Registry. Dissemination of the findings will include peer-reviewed publications, conference presentations and media releases.

TRIAL REGISTRATION NUMBER: ChiCTR2300068786.

PMID:37821136 | DOI:10.1136/bmjopen-2023-075332

Food Chem Toxicol. 2023 Oct 9:114086. doi: 10.1016/j.fct.2023.114086. Online ahead of print.

ABSTRACT

Humans are constantly exposed to lipophilic persistent organic pollutants (POPs) that accumulate in fatty foods. Among the numerous POPs, dioxins, in particular 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can impact several organ systems. While the hazard is clearly recognized, it is still difficult to develop a comprehensive understanding of the overall health impacts of dioxins. As chemical toxicity testing is steadily adopting new approach methodologies (NAMs), it becomes imperative to develop computational models that can bridge the data gaps between in vitro testing and in vivo outcomes. As an effort to address this challenge, we propose a multiscale computational approach using a "template-and-anchor" (T&A) structure. A template is a high-level umbrella model that permits the integration of information from various, detailed anchor models. In the present study, we use this T&A approach to describe the effect of TCDD on cholesterol dynamics. Specifically, we represent hepatic cholesterol biosynthesis as an anchor model that is perturbed by TCDD, leading to steatosis, along with alterations of plasma cholesterol. Incorporating pertinent information from all anchor models into the template model will in future allow the characterization of the global effects of dioxin, which can subsequently be translated into overall - and ultimately personalized - human health risk assessment.

PMID:37820785 | DOI:10.1016/j.fct.2023.114086

Cell Syst. 2023 Oct 6:S2405-4712(23)00268-5. doi: 10.1016/j.cels.2023.09.003. Online ahead of print.

ABSTRACT

Our knowledge of transcriptional responses to changes in nutrient availability comes primarily from few well-studied transcription factors (TFs), often lacking an unbiased genome-wide perspective. Leveraging recent advances allowing bacterial genomic footprinting, we comprehensively mapped the genome-wide regulatory responses of Escherichia coli to exogenous leucine, methionine, alanine, and lysine. The global TF Lrp was found to individually sense three amino acids and mount three different target gene responses. Overall, 531 genes had altered RNA polymerase occupancy, and 32 TFs responded directly or indirectly to the presence of amino acids, including regulators of membrane and osmotic pressure homeostasis. About 70% of the detected TF-DNA interactions had not been reported before. We thus identified 682 previously unknown TF-binding locations, for a subset of which the involved TFs were identified by affinity purification. This comprehensive map of amino acid regulation illustrates the incompleteness of the known transcriptional regulation network, even in E. coli.

PMID:37820729 | DOI:10.1016/j.cels.2023.09.003