ArXiv [Preprint]. 2024 Jul 11:arXiv:2407.08612v1.

ABSTRACT

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands of parameters depending on the complexity of the biological system modeled, potentially making the task of fitting parameters to the model difficult - especially when new experimental data cannot be gathered. We demonstrate a method that uses structural biology predictions to augment systems biology models to improve systems biology models' predictions without having to gather more experimental data. Additionally, we show how systems biology models' predictions can help evaluate novel structural biology hypotheses, which may also be expensive or infeasible to validate.

PMID:39040647 | PMC:PMC11261965

Front Oncol. 2024 Jul 8;14:1384061. doi: 10.3389/fonc.2024.1384061. eCollection 2024.

ABSTRACT

INTRODUCTION: The impact of the COVID-19 pandemic on head and neck cancer (HNC) has been suggested, but the causal relationship remains unclear.

METHODS: We explore this connection by utilizing the Mendelian randomization (MR) approach applied to publicly available genome-wide association study (GWAS) summary datasets for COVID-19 and HNC. The datasets included critical COVID-19 (13,769 cases, 1,072,442 controls), hospitalized COVID-19 (32,519 cases, 2,062,805 controls), SARS-CoV-2 infection (122,616 cases, 2,475,240 controls), and HNC (2,131 cases, 287,137 controls). Mechanistic underpinnings of the causal relationships identified by MR analysis were explored through functional annotation augmented by AI-based literature data mining.

RESULTS: Surprisingly, a genetic predisposition to contracting a milder form of COVID-19 substantially reduced the risks of developing HNC (OR: 0.52, 95% CI: 0.35-0.78, p = 1.42E-03), with no significant association between genetic liability to severe COVID-19 and the risk of HNC detected. Additionally, our findings highlighted 14 genes linked to SARS-CoV-2 infection, potentially playing a protective role in the context of HNC. These genes include OAS1, LOC107985887, BCL11A, DPP9, LOC107984685, LINC02326, MUC4, NXPE3, IFNAR2, LZTFL1, LOC105372437, NAPSA, LOC105376622, LOC107986082, and SLC6A20.

CONCLUSION: Our study emphasizes the protective role of the genetic liability to milder COVID-19 in reducing the risk of HNC while refuting a causal relationship between severe COVID-19 and HNC.

PMID:39040446 | PMC:PMC11260674 | DOI:10.3389/fonc.2024.1384061

iScience. 2024 May 22;27(7):110077. doi: 10.1016/j.isci.2024.110077. eCollection 2024 Jul 19.

ABSTRACT

Lymph node metastasis (LNM) is the main metastatic pathway of cervical cancer, which is closely related to 5-year survival rate of cervical squamous cell carcinoma (CSCC), yet the underlying mechanism remains unconfirmed. In this study, we show that midkine (MDK) was highly expressed in CSCC and overexpression of MDK was associated with CSCC LNM. Functional investigations demonstrated that MDK promoted LNM by enhancing proliferation, migration and invasion capacity of cervical cancer cells, facilitating lymphangiogenesis and down-regulating the expression of tight junction proteins of human lymphatic endothelial cells (HLECs). MDK exerted these biological effects by interacting with Syndecan-1 and activating PI3K/AKT and p38 MAPK pathways. A retrospective study showed that s-MDK was related to LNM. s-MDK combined with serum-squamous cell carcinoma antigen(s-SCCA) improved the diagnostic accuracy of CSCC LNM. These findings established a new mechanism of LNM and highlighted MDK as a candidate tumor biomarker and therapeutic target in CSCC.

PMID:39040052 | PMC:PMC11261016 | DOI:10.1016/j.isci.2024.110077

Small Methods. 2024 Jul 23:e2400633. doi: 10.1002/smtd.202400633. Online ahead of print.

ABSTRACT

Lipid nanoparticles encapsulating mRNA (LNP-mRNA) revolutionized medicine over the past several years. While clinically approved indications currently focus on infectious disease vaccination, LNP-mRNA based treatments also hold promise for cancer immunotherapy. However, the route of dosing may impact treatment efficacy, safety, and dose. To minimize adverse effects, it is hypothesized that LNP-mRNA can be used to activate and engineer dendritic cells (DC) ex vivo before re-administration of these cells. Here, it is shown that LNP-mRNA engineered DCs can indeed vaccinate recipient mice. Vaccinated mice showed strong anti-tumor T cell responses, rejected tumor challenge, and displayed no evidence of toxicity. Further, it is found that DC specific ablation of the immune activating kinase NFkB inducing kinase (NIK) abrogated vaccination efficacy, demonstrating that adoptively transferred DCs can be functionally modified in addition to their antigen presentation capacity. Collectively, these studies show that ex vivo LNP-mRNA engineering of DCs is a feasible and robust therapeutic strategy for cancer.

PMID:39039995 | DOI:10.1002/smtd.202400633

Stem Cell Res Ther. 2024 Jul 23;15(1):220. doi: 10.1186/s13287-024-03840-y.

NO ABSTRACT

PMID:39039585 | DOI:10.1186/s13287-024-03840-y

Methods Mol Biol. 2024;2824:409-424. doi: 10.1007/978-1-0716-3926-9_26.

ABSTRACT

Three-dimensional culture models of the brain enable the study of neuroinfection in the context of a complex interconnected cell matrix. Depending on the differentiation status of the neural cells, two models exist: 3D spheroids also called neurospheres and cerebral organoids. Here, we describe the preparation of 3D spheroids and cerebral organoids and give an outlook on their usage to study Rift Valley fever virus and other neurotropic viruses.

PMID:39039427 | DOI:10.1007/978-1-0716-3926-9_26

Methods Mol Biol. 2024;2824:361-372. doi: 10.1007/978-1-0716-3926-9_22.

ABSTRACT

On the RNA level, viral infections are characterized by perturbations in the host cell transcriptome as well as the development of viral genetic information. Investigating the abundance and dynamic of RNA molecules can provide ample information to understand many aspects of the infection, from viral replication to pathogenesis. A key aspect therein is the resolution of the data, as infections are generally highly heterogeneous. Even in simple model systems such as cell lines, viral infections happen in a very asynchronous way. Quantifying RNAs at single-cell resolution can therefore substantially increase our understanding of these processes.Whereas measuring the RNA in bulk, that is, in samples containing thousands to hundreds of thousands of cells, is established and widely used since many years, methods for studying not only just a few different RNAs in individual cells became widely available only recently. Here, I outline and compare current concepts and methodologies for using single-cell RNA-sequencing to study virus infections. This covers sample preparation, cell preservation, biosafety considerations, and various experimental methods, with a special focus on the aspects that are important for studying virus infections. Since there is not "the one" method for doing single-cell RNA-sequencing, I will not provide a detailed protocol. Rather, this chapter should serve as a primer for getting started with single-cell RNA-sequencing experiments of virus infections and discusses the criteria that allow readers to choose the best procedures for their specific research question.

PMID:39039423 | DOI:10.1007/978-1-0716-3926-9_22

Methods Mol Biol. 2024;2824:221-239. doi: 10.1007/978-1-0716-3926-9_15.

ABSTRACT

Cellular electron cryo-tomography (cryoET) produces high-resolution three-dimensional images of subcellular structures in a near-native frozen-hydrated state. These three-dimensional images are obtained by recording a series of two-dimensional tilt images on a transmission electron cryo-microscope that are subsequently back-projected to form a tomogram. Key to a successful experiment is however a high-quality sample. This chapter outlines a basic workflow for the preparation of cellular cryoET samples. It covers the preparation of infected cells on electron cryo-microscopy grids and the vitrification by plunge-freezing and clipping of grids into AutoGrid rims. It also provides a general overview of the workflow for thinning the vitrified cells by focused ion beam (FIB) milling. Although this book is dedicated to Rift Valley fever virus research, the present protocol may also be applied to any other research subject where high-resolution structural insight into intracellular processes is desired.

PMID:39039416 | DOI:10.1007/978-1-0716-3926-9_15

Nat Med. 2024 Jul 22. doi: 10.1038/s41591-024-03142-z. Online ahead of print.

ABSTRACT

For many diseases there are delays in diagnosis due to a lack of objective biomarkers for disease onset. Here, in 41,931 individuals from the United Kingdom Biobank Pharma Proteomics Project, we integrated measurements of ~3,000 plasma proteins with clinical information to derive sparse prediction models for the 10-year incidence of 218 common and rare diseases (81-6,038 cases). We then compared prediction models developed using proteomic data with models developed using either basic clinical information alone or clinical information combined with data from 37 clinical assays. The predictive performance of sparse models including as few as 5 to 20 proteins was superior to the performance of models developed using basic clinical information for 67 pathologically diverse diseases (median delta C-index = 0.07; range = 0.02-0.31). Sparse protein models further outperformed models developed using basic information combined with clinical assay data for 52 diseases, including multiple myeloma, non-Hodgkin lymphoma, motor neuron disease, pulmonary fibrosis and dilated cardiomyopathy. For multiple myeloma, single-cell RNA sequencing from bone marrow in newly diagnosed patients showed that four of the five predictor proteins were expressed specifically in plasma cells, consistent with the strong predictive power of these proteins. External replication of sparse protein models in the EPIC-Norfolk study showed good generalizability for prediction of the six diseases tested. These findings show that sparse plasma protein signatures, including both disease-specific proteins and protein predictors shared across several diseases, offer clinically useful prediction of common and rare diseases.

PMID:39039249 | DOI:10.1038/s41591-024-03142-z

Clin Mol Hepatol. 2024 Jul 23. doi: 10.3350/cmh.2024.0333. Online ahead of print.

ABSTRACT

INTRODUCTION: Combination immunotherapy, exemplified by atezolizumab plus bevacizumab, has become the standard of care for inoperable hepatocellular carcinoma (HCC). However, the lack of predictive biomarkers and limited understanding of response mechanisms remain a challenge.

METHODS: Using data from the IMbrave150plus cohort, we applied an immune signature score (ISS) predictor to stratify HCC patients treated with atezolizumab plus bevacizumab or with sorafenib alone into potential high and low response groups. By applying multiple statistical approaches including a Bayesian covariate prediction algorithm, we refined the signature to 10 key genes (ISS10) for clinical use while maintaining similar predictive power to the full model. We further validated ISS10 in an independent HCC cohort treated with nivolumab plus ipilimumab.

RESULTS: The study identified a significant association between the ISS and treatment response. Among patients classified as high responders, those treated with the atezolizumab plus bevacizumab combination exhibited improved overall and progression-free survival as well as better objective response rate compared to those treated with sorafenib. We also observed a significant correlation between ISS10 and response to nivolumab plus ipilimumab treatment. Analysis of immune cell subpopulations revealed distinct characteristics associated with ISS subtypes. In particular, the ISS10 high subtype displayed a more favorable immune environment with higher proportions of anti-tumor macrophages and activated T-cells, potentially explaining its better response.

CONCLUSIONS: Our study suggests that ISS and ISS10 are promising predictive biomarkers for enhanced therapeutic outcomes in HCC patients undergoing combination immunotherapy. These markers are crucial for refining patient stratification and personalized treatment approaches to advance the effectiveness of standard-of-care regimens.

PMID:39038962 | DOI:10.3350/cmh.2024.0333

Biotechnol Adv. 2024 Jul 20:108417. doi: 10.1016/j.biotechadv.2024.108417. Online ahead of print.

ABSTRACT

Protein expression is a critical process in diverse biological systems. For Escherichia coli, a widely employed microbial host in industrial catalysis and healthcare, researchers often face significant challenges in constructing recombinant expression systems. To maximize the potential of E. coli expression systems, it is essential to address problems regarding the low or absent production of certain target proteins. This article presents viable solutions to the main factors posing challenges to heterologous protein expression in E. coli, which includes protein toxicity, the intrinsic influence of gene sequences, and mRNA structure. These strategies include specialized approaches for managing toxic protein expression, addressing issues related to mRNA structure and codon bias, advanced codon optimization methodologies that consider multiple factors, and emerging optimization techniques facilitated by big data and machine learning.

PMID:39038691 | DOI:10.1016/j.biotechadv.2024.108417

Pharmacol Res. 2024 Jul 20:107321. doi: 10.1016/j.phrs.2024.107321. Online ahead of print.

ABSTRACT

The critical role of the gut microbiome in gastrointestinal cancers is becoming increasingly clear. Imbalances in the gut microbial community, referred to as dysbiosis, are linked to increased risks for various forms of gastrointestinal cancers. Pathogens like Fusobacterium and Helicobacter pylori relate to the onset of esophageal and gastric cancers, respectively, while microbes such as Porphyromonas gingivalis and Clostridium species have been associated with a higher risk of pancreatic cancer. In colorectal cancer, bacteria such as Fusobacterium nucleatum are known to stimulate the growth of tumor cells and trigger cancer-promoting pathways. On the other hand, beneficial microbes like Bifidobacteria offer a protective effect, potentially inhibiting the development of gastrointestinal cancers. The potential for therapeutic interventions that manipulate the gut microbiome is substantial, including strategies to engineer anti-tumor metabolites and employ microbiota-based treatments. Despite the progress in understanding the influence of the microbiome on gastrointestinal cancers, significant challenges remain in identifying and understanding the precise contributions of specific microbial species and their metabolic products. This knowledge is essential for leveraging the role of the gut microbiome in the development of precise diagnostics and targeted therapies for gastrointestinal cancers.

PMID:39038631 | DOI:10.1016/j.phrs.2024.107321

Elife. 2024 Jul 22;13:e94007. doi: 10.7554/eLife.94007.

ABSTRACT

Bats have unique characteristics compared to other mammals, including increased longevity and higher resistance to cancer and infectious disease. While previous studies have analyzed the metabolic requirements for flight, it is still unclear how bat metabolism supports these unique features, and no study has integrated metabolomics, transcriptomics, and proteomics to characterize bat metabolism. In this work, we performed a multi-omics data analysis using a computational model of metabolic fluxes to identify fundamental differences in central metabolism between primary lung fibroblast cell lines from the black flying fox fruit bat (Pteropus alecto) and human. Bat cells showed higher expression levels of Complex I components of electron transport chain (ETC), but, remarkably, a lower rate of oxygen consumption. Computational modeling interpreted these results as indicating that Complex II activity may be low or reversed, similar to an ischemic state. An ischemic-like state of bats was also supported by decreased levels of central metabolites and increased ratios of succinate to fumarate in bat cells. Ischemic states tend to produce reactive oxygen species (ROS), which would be incompatible with the longevity of bats. However, bat cells had higher antioxidant reservoirs (higher total glutathione and higher ratio of NADPH to NADP) despite higher mitochondrial ROS levels. In addition, bat cells were more resistant to glucose deprivation and had increased resistance to ferroptosis, one of the characteristics of which is oxidative stress. Thus, our studies revealed distinct differences in the ETC regulation and metabolic stress responses between human and bat cells.

PMID:39037770 | DOI:10.7554/eLife.94007

Liver Int. 2024 Jul 22. doi: 10.1111/liv.16021. Online ahead of print.

NO ABSTRACT

PMID:39037222 | DOI:10.1111/liv.16021

Anal Methods. 2024 Jul 22. doi: 10.1039/d4ay00810c. Online ahead of print.

ABSTRACT

Fourier-transform infrared (FTIR) spectroscopy is a simple, fast and inexpensive method with a history of use for bacterial analysis. However, due to the limitations placed on spatial resolution inherent to infrared wavelengths, analysis has generally been performed on bulk samples, leading to biological variance among individual cells to be buried in averaged spectra. This also increases the bacterial load necessary for analysis, which can be problematic in clinical settings where limiting incubation time is valuable. Optical photothermal-induced resonance (O-PTIR) spectroscopy is a novel method aiming to bypass this limitation using a secondary lower wavelength laser, allowing for infrared measurements of a single bacterium. Here, using Staphylococcus capitis, Staphylococcus epidermidis and Micrococcus luteus strains as a model and FTIR as a benchmark, we examined O-PTIR's ability to discriminate single-cell samples at the intergenetic, interspecific and intraspecific levels. When combined with chemometric analysis, we showed that O-PTIR is capable of discriminating different between genera, species and strains within species to a degree comparable with FTIR. Furthermore, small variations in the amide bands associated with differences in the protein structure can still be seen in spite of smaller sample sizes. This demonstrates the potential of O-PTIR for single-cell bacterial analysis and classification.

PMID:39037041 | DOI:10.1039/d4ay00810c

Development. 2024 Jul 15;151(14):dev202800. doi: 10.1242/dev.202800. Epub 2024 Jul 18.

ABSTRACT

We present a new set of computational tools that enable accurate and widely applicable 3D segmentation of nuclei in various 3D digital organs. We have developed an approach for ground truth generation and iterative training of 3D nuclear segmentation models, which we applied to popular CellPose, PlantSeg and StarDist algorithms. We provide two high-quality models trained on plant nuclei that enable 3D segmentation of nuclei in datasets obtained from fixed or live samples, acquired from different plant and animal tissues, and stained with various nuclear stains or fluorescent protein-based nuclear reporters. We also share a diverse high-quality training dataset of about 10,000 nuclei. Furthermore, we advanced the MorphoGraphX analysis and visualization software by, among other things, providing a method for linking 3D segmented nuclei to their surrounding cells in 3D digital organs. We found that the nuclear-to-cell volume ratio varies between different ovule tissues and during the development of a tissue. Finally, we extended the PlantSeg 3D segmentation pipeline with a proofreading tool that uses 3D segmented nuclei as seeds to correct cell segmentation errors in difficult-to-segment tissues.

PMID:39036998 | DOI:10.1242/dev.202800

Iran Biomed J. 2024 Jun 29. doi: 10.61186/ibj.4177. Online ahead of print.

ABSTRACT

BACKGROUND: Cutaneous leishmaniasis is a major health problem caused by an intracellular pathogen of the genus Leishmania. CL results in morphologically distinct skin injuries, ranging from nodules to plaques and ulcers, which persist as a recuperating incessant injury depending on the type of contaminating parasite. There is still no effective treatment to reduce the skin lesions in patients infected with CL. The aim of this study was to develop strategies to treat skin lesions in CL patients.

METHODS: We retrieved the transcriptomic data of skin lesions from patients with CL and normal skin from the GEO database. The PPIN was constructed using the STRING database and Cytoscape v3.10.1 software. Critical genes were identified by topological network analysis and cluster detection. Finally, gene ontology and repurposing drugs for critical genes were determined.

RESULTS: CD8A, IFNG, IL-6, PTPRC, CCR7, TLR2, GSTA5, CYBB, IL-12RB2, ITGB2, FCGR3A, CTLA4, and IFNG were identified as the critical genes in PPIN and subnetworks. Enrichment analysis revealed that T-cell receptor signaling, TLR signaling, cytokine-cytokine receptor interaction, graft-versus-host disease, leishmaniasis, chemokine signaling, primary immunodeficiency, and Th17 cell differentiation were the major pathways associated with critical genes. The drug repurposing results identified cyclosporine, rituximab, infliximab, blinatumomab, and methylprednisolone as candidates for treatment of CL.

CONCLUSION: After validating our model with available experimental data, we found that critical molecules and drug candidates play a crucial role in the treatment of skin lesions caused by Leishmania in prospective studies.

PMID:39036455 | DOI:10.61186/ibj.4177

Chem. 2024 Jul 11;10(7):2220-2244. doi: 10.1016/j.chempr.2024.03.015. Epub 2024 Apr 12.

ABSTRACT

Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.

PMID:39036067 | PMC:PMC11259118 | DOI:10.1016/j.chempr.2024.03.015

Curr Zool. 2023 Jul 3;70(3):291-297. doi: 10.1093/cz/zoad029. eCollection 2024 Jun.

ABSTRACT

The search for common characteristics between the musical abilities of humans and other animal species is still taking its first steps. One of the most promising aspects from a comparative point of view is the analysis of rhythmic components, which are crucial features of human communicative performance but also well-identifiable patterns in the vocal displays of other species. Therefore, the study of rhythm is becoming essential to understand the mechanisms of singing behavior and the evolution of human communication. Recent findings provided evidence that particular rhythmic structures occur in human music and some singing animal species, such as birds and rock hyraxes, but only 2 species of nonhuman primates have been investigated so far (Indri indri and Hylobates lar). Therefore, our study aims to consistently broaden the list of species studied regarding the presence of rhythmic categories. We investigated the temporal organization in the singing of 3 species of crested gibbons (Nomascus gabriellae, Nomascus leucogenys, and Nomascus siki) and found that the most prominent rhythmic category was isochrony. Moreover, we found slight variation in songs' tempo among species, with N. gabriellae and N. siki singing with a temporal pattern involving a gradually increasing tempo (a musical accelerando), and N. leucogenys with a more regular pattern. Here, we show how the prominence of a peak at the isochrony establishes itself as a shared characteristic in the small apes considered so far.

PMID:39035758 | PMC:PMC11255994 | DOI:10.1093/cz/zoad029

J Pharm Anal. 2024 Jun;14(6):100916. doi: 10.1016/j.jpha.2023.12.006. Epub 2023 Dec 10.

ABSTRACT

In this review, we focus on providing basics and examples for each component of the protein therapeutic specifications to interested pharmacists and biopharmaceutical scientists with a goal to strengthen understanding in regulatory science and compliance. Pharmaceutical specifications comprise a list of important quality attributes for testing, references to use for test procedures, and appropriate acceptance criteria for the tests, and they are set up to ensure that when a drug product is administered to a patient, its intended therapeutic benefits and safety can be rendered appropriately. Conformance of drug substance or drug product to the specifications is achieved by testing an article according to the listed tests and analytical methods and obtaining test results that meet the acceptance criteria. Quality attributes are chosen to be tested based on their quality risk, and consideration should be given to the merit of the analytical methods which are associated with the acceptance criteria of the specifications. Acceptance criteria are set forth primarily based on efficacy and safety profiles, with an increasing attention noted for patient-centric specifications. Discussed in this work are related guidelines that support the biopharmaceutical specification setting, how to set the acceptance criteria, and examples of the quality attributes and the analytical methods from 60 articles and 23 pharmacopeial monographs. Outlooks are also explored on process analytical technologies and other orthogonal tools which are on-trend in biopharmaceutical characterization and quality control.

PMID:39035218 | PMC:PMC11259812 | DOI:10.1016/j.jpha.2023.12.006