Nanomaterials (Basel). 2024 Dec 4;14(23):1945. doi: 10.3390/nano14231945.

ABSTRACT

We previously described GMC, a graphene-based nanomaterial obtained from carbon nanofibers (CNFs), to be biologically compatible and functional for therapeutic purposes. GMC can reduce triglycerides' content in vitro and in vivo and has other potential bio-functional effects on systemic cells and the potential utility to be used in living systems. Here, immunoreactivity was evaluated by adding GMC in suspension at the biologically functional concentrations, ranging from 10 to 60 µg/mL, for one or several days, to cultured lymphocytes (T, B, NK), either in basal or under stimulating conditions, and monocytes that were derived under culture conditions to pro-inflammatory (GM-MØ) or anti-inflammatory (M-MØ) macrophages. All stirpes were obtained from human peripheral mononuclear cells (PBMCs) from anonymized healthy donors. The viability (necrosis, apoptosis) and immunological activity of each progeny was analyzed using either flow cytometry and/or other analytical determinations. A concentration of 10 to 60 µg/mL GMC did not affect lymphocytes' viability, either in basal or active conditions, during one or more days of treatment. The viability and expression of the inflammatory interleukin IL-1β in the monocyte cell line THP-1 were not affected. Treatments with 10 or 20 µg/mL GMC on GM-MØ or M-MØ during or after their differentiation process promoted phagocytosis, but their viability and the release of the inflammatory marker activin A by GM-MØ were not affected. A concentration of 60 µg/mL GMC slightly increased macrophages' death and activity in some culture conditions. The present work demonstrates that GMC is safe or has minimal immunological activity when used in suspension at low concentrations for pre-clinical or clinical settings. Its biocompatibility will depend on the dose, formulation or way of administration and opens up the possibility to consider GMC or other CNF-based biomaterials for innovative therapeutic strategies.

PMID:39683333 | DOI:10.3390/nano14231945

Foods. 2024 Nov 30;13(23):3880. doi: 10.3390/foods13233880.

ABSTRACT

Sodium benzoate (E211) and potassium sorbate (E202) are two preservatives widely used alone or in combination in the food industry in Algeria. This study aims to estimate the dietary exposure of children and adolescents to these substances in Oran Province (Algeria) and to assess the risks incurred in consuming these two preservatives. For this, a total of 116 commercial food samples were analyzed for potassium sorbate and sodium benzoate content by HPLC, and a survey was carried out on 250 children and 765 adolescents using a consumption frequency questionnaire as the method. The concentration of preservatives in foodstuffs was mostly within the maximum permitted limits set by national and international standards. In scenario 2 and scenario 3, the estimated average dietary exposure to the two preservatives was below the ADI: it was 17-48% and 21-36% of the ADI for potassium sorbate and sodium benzoate, respectively. The dietary exposure at the 95th percentile exceeded the ADI for sodium benzoate and potassium sorbate when calculations were made using the average of samples containing these preservatives. The main contributors to exposure were carbonated drinks for sodium benzoate and juices, cheeses, and yogurts for potassium sorbate.

PMID:39682951 | DOI:10.3390/foods13233880

Foods. 2024 Nov 25;13(23):3781. doi: 10.3390/foods13233781.

ABSTRACT

Goat milk butter, locally known as "Dhan", from the Sfisfa region of Algeria, holds significant cultural and economic value. This study investigates the probiotic properties of lactic acid bacteria (LAB) present in Dhan, focusing particularly on Lactobacillus strains. Molecular identification using 16S rRNA revealed a dominance of Levilactobacillus brevis and Lactiplantibacillus plantarum, forming a substantial part of the bacterial profile. Three LAB isolates (DC01-A, DC04, and DC06) were selected from fresh samples, and rigorous analyses were performed to evaluate their probiotic properties. Safety assessments confirmed the absence of gelatinase, DNase, and haemolytic activities in all isolates. The isolates demonstrated high tolerance to bile salts and acidic conditions, along with the ability to survive simulated gastrointestinal digestion. Notably, strain DC06 exhibited exceptional survival at low pH (1.5) and high bile salt concentrations (0.15-0.3%). All isolates showed substantial growth in MRS medium with 2% phenol, although growth was significantly decreased at 5% phenol. Furthermore, our strains exhibited high adhesion rates to various solvents, demonstrating their potential for strong interaction with cell membranes. Specifically, adhesion to chloroform was observed at 98.26% for DC01-A, 99.30% for DC04, and 99.20% for DC06. With xylene, the adhesion rates were 75.94% for DC01-A, 61.13% for DC04, and 76.52% for DC06. The LAB strains demonstrated impressive growth in ethanol concentrations up to 12%, but their tolerance did not exceed this concentration. They also exhibited robust growth across temperatures from 10 °C to 37 °C, with strains DC04 and DC06 able to proliferate at 45 °C, though none survived at 50 °C. Additionally, the isolates showed significant resistance to oxidative stress induced by hydrogen peroxide (H2O2) and displayed medium to high autolytic activity, with rates of 50.86%, 37.53%, and 33.42% for DC01-A, DC04, and DC06, respectively. The cell-free supernatant derived from strain DC04 exhibited significant antimicrobial activity against the tested pathogens, while strain DC06 demonstrated moderate antioxidant activity with the highest DPPH scavenging rate at 68.56%, compared to the probiotic reference strain LGG at 61.28%. These collective findings not only suggest the probiotic viability of LAB strains found in Dhan but also highlight the importance of traditional food practises in contributing to health and nutrition. Consequently, this study supports the potential of traditional Dhan butter as a functional food and encourages further exploration of its health benefits.

PMID:39682853 | DOI:10.3390/foods13233781

Diagnostics (Basel). 2024 Nov 23;14(23):2640. doi: 10.3390/diagnostics14232640.

ABSTRACT

Late-onset Alzheimer's disease (LOAD) is a subtype of dementia that manifests after the age of 65. It is characterized by progressive impairments in cognitive functions, behavioral changes, and learning difficulties. Given the progressive nature of the disease, early diagnosis is crucial. Early-onset Alzheimer's disease (EOAD) is solely attributable to genetic factors, whereas LOAD has multiple contributing factors. A complex pathway mechanism involving multiple factors contributes to LOAD progression. Employing a systems biology approach, our analysis encompassed the genetic, epigenetic, metabolic, and environmental factors that modulate the molecular networks and pathways. These factors affect the brain's structural integrity, functional capacity, and connectivity, ultimately leading to the manifestation of the disease. This study has aggregated diverse biomarkers associated with factors capable of altering the molecular networks and pathways that influence brain structure, functionality, and connectivity. These biomarkers serve as potential early indicators for AD diagnosis and are designated as early biomarkers. The other biomarker datasets associated with the brain structure, functionality, connectivity, and related parameters of an individual are broadly categorized as clinical-stage biomarkers. This study has compiled research papers on Alzheimer's disease (AD) diagnosis utilizing machine learning (ML) methodologies from both categories of biomarker data, including the applications of ML techniques for AD diagnosis. The broad objectives of our study are research gap identification, assessment of biomarker efficacy, and the most effective or prevalent ML technology used in AD diagnosis. This paper examines the predominant use of deep learning (DL) and convolutional neural networks (CNNs) in Alzheimer's disease (AD) diagnosis utilizing various types of biomarker data. Furthermore, this study has addressed the potential scope of using generative AI and the Synthetic Minority Oversampling Technique (SMOTE) for data augmentation.

PMID:39682548 | DOI:10.3390/diagnostics14232640

Cancers (Basel). 2024 Dec 6;16(23):4095. doi: 10.3390/cancers16234095.

ABSTRACT

Pancreatic ductal adenocarcinoma (PDAC) stands as one of the most lethal cancers, marked by rapid progression, pronounced chemoresistance, and a complex network of genetic and epigenetic dysregulation. Within this challenging context, sirtuins, NAD+-dependent deacetylases, have emerged as pivotal modulators of key cellular processes that drive pancreatic cancer progression. Each sirtuin contributes uniquely to PDAC pathogenesis. SIRT1 influences apoptosis and chemoresistance through hypoxia, enhancing glycolytic metabolism and HIF-1α signaling, which sustain tumor survival against drugs like gemcitabine. SIRT2, conversely, disrupts cancer cell proliferation by inhibiting eIF5A, while SIRT3 exerts tumor-suppressive effects by regulating mitochondrial ROS and glycolysis. SIRT4 inhibits aerobic glycolysis, and its therapeutic upregulation has shown promise in curbing PDAC progression. Furthermore, SIRT5 modulates glutamine and glutathione metabolism, offering an avenue to disrupt PDAC's metabolic dependencies. SIRT6 and SIRT7, through their roles in angiogenesis, EMT, and metastasis, represent additional targets, with modulators of SIRT6, such as JYQ-42, showing potential to reduce tumor invasiveness. This review aims to provide a comprehensive exploration of the emerging roles of sirtuins, a family of NAD+-dependent enzymes, as critical regulators within the oncogenic landscape of pancreatic cancer. This review meticulously explores the nuanced involvement of sirtuins in pancreatic cancer, elucidating their contributions to tumorigenesis and suppression through mechanisms such as metabolic reprogramming, the maintenance of genomic integrity and epigenetic modulation. Furthermore, it emphasizes the urgent need for the development of targeted therapeutic interventions aimed at precisely modulating sirtuin activity, thereby enhancing therapeutic efficacy and optimizing patient outcomes in the context of pancreatic malignancies.

PMID:39682281 | DOI:10.3390/cancers16234095

Nat Struct Mol Biol. 2024 Dec 16. doi: 10.1038/s41594-024-01431-2. Online ahead of print.

ABSTRACT

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

PMID:39681766 | DOI:10.1038/s41594-024-01431-2

Nat Biotechnol. 2024 Dec 16. doi: 10.1038/s41587-024-02512-9. Online ahead of print.

ABSTRACT

Pooled genetic screening with CRISPR-Cas9 has enabled genome-wide, high-resolution mapping of genes to phenotypes, but assessing the effect of a given genetic perturbation requires evaluation of each single guide RNA (sgRNA) in hundreds of cells to counter stochastic genetic drift and obtain robust results. However, resolution is limited in complex, heterogeneous models, such as organoids or tumors transplanted into mice, because achieving sufficient representation requires impractical scaling. This is due to bottleneck effects and biological heterogeneity of cell populations. Here we introduce CRISPR-StAR, a screening method that uses internal controls generated by activating sgRNAs in only half the progeny of each cell subsequent to re-expansion of the cell clone. Our method overcomes both intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by generating clonal, single-cell-derived intrinsic controls. We use CRISPR-StAR to identify in-vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking against conventional screening demonstrates the improved data quality provided by this technology.

PMID:39681701 | DOI:10.1038/s41587-024-02512-9

Nat Neurosci. 2024 Dec 16. doi: 10.1038/s41593-024-01858-2. Online ahead of print.

NO ABSTRACT

PMID:39681663 | DOI:10.1038/s41593-024-01858-2

Sci Rep. 2024 Dec 16;14(1):30493. doi: 10.1038/s41598-024-81972-0.

ABSTRACT

The extracellular parasite Trypanosoma brucei evades the immune system of the mammalian host by periodically exchanging its variant surface glycoprotein (VSG) coat. Hereby, only one VSG gene is transcribed from one of 15 subtelomeric so-called bloodstream form expression sites (BES) at any given timepoint, while all other BESs are silenced. VSG gene expression is altered by homologous recombination using a large VSG gene repertoire or by a so-called in situ switch, which activates a previously silent BES. Transcriptional activation, VSG switching and VSG silencing during developmental differentiation from the bloodstream form to the procyclic form present in the tsetse fly vector are tightly regulated. Due to their subtelomeric position, telomere-associated proteins are involved in the regulation of VSG expression. Three functional homologs of mammalian telomere complex proteins have been characterized thus far, and novel telomere-interacting proteins, such as telomere-associated protein 1 (TelAP1), have recently been identified. Here, we used mass spectrometry-based proteomics and interactomics approaches, telomere pull-down assays with recombinant material and immunofluorescence analysis to elucidate the interactions of 21 other putative TelAPs. We investigated the influence on VSG expression and showed that depletion of TelAPs does not ultimately lead to changes in VSG expression. Additionally, we examined the interaction patterns of four TelAPs with the TbTRF/TbTIF2/TbRAP1 telomere complex by reciprocal affinity purification. We further propose that TelAP1 interacts with Tb927.6.4330, now called TelAP2, and that TelAP1 depends on this interaction to form a complex with the telomeric proteins TbTRF, TbTIF2 and TbRAP1.

PMID:39681615 | DOI:10.1038/s41598-024-81972-0

Commun Med (Lond). 2024 Dec 16;4(1):265. doi: 10.1038/s43856-024-00637-1.

ABSTRACT

BACKGROUND: Distal sensorimotor polyneuropathy (DSPN) is a common neurological disorder in elderly adults and people with obesity, prediabetes and diabetes and is associated with high morbidity and premature mortality. DSPN is a multifactorial disease and not fully understood yet.

METHODS: Here, we developed the Interpretable Multimodal Machine Learning (IMML) framework for predicting DSPN prevalence and incidence based on sparse multimodal data. Exploiting IMMLs interpretability further empowered biomarker identification. We leveraged the population-based KORA F4/FF4 cohort including 1091 participants and their deep multimodal characterisation, i.e. clinical data, genomics, methylomics, transcriptomics, proteomics, inflammatory proteins and metabolomics.

RESULTS: Clinical data alone is sufficient to stratify individuals with and without DSPN (AUROC = 0.752), whilst predicting DSPN incidence 6.5 ± 0.2 years later strongly benefits from clinical data complemented with two or more molecular modalities (improved ΔAUROC > 0.1, achieved AUROC of 0.714). Important and interpretable features of incident DSPN prediction include up-regulation of proinflammatory cytokines, down-regulation of SUMOylation pathway and essential fatty acids, thus yielding novel insights in the disease pathophysiology.

CONCLUSIONS: These may become biomarkers for incident DSPN, guide prevention strategies and serve as proof of concept for the utility of IMML in studying complex diseases.

PMID:39681608 | DOI:10.1038/s43856-024-00637-1

Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2415315121. doi: 10.1073/pnas.2415315121. Epub 2024 Dec 16.

ABSTRACT

In view of changing climatic conditions and disappearing natural resources such as fertile soil and water, exploring alternatives to today's industrial monocrop farming becomes essential. One promising farming practice is intercropping (IC), in which two or more crop species are grown together. Many experiments have shown that, under certain circumstances, IC can decrease soil erosion and fertilizer use, improve soil health and land management, while preserving crop production levels. However, there have been no quantitative approaches to predict, design, and control appropriate IC implementation for given particular environmental and farming conditions, and to assess its robustness. Here, we develop such an approach, based on methods and concepts developed in data science and systems biology. Our dataset groups the results of 2258 IC experiments, involving 274 pairs of 69 different plants. The data include 4 soil characteristics and 5 environmental and farming conditions, together with 8 traits for each of the two intercropped plants. We performed a dimensional reduction of the resulting 25-dimensional variable space and showed that, from a few quantities, one can predict IC yield relative to sole cultivation with good accuracy. For given environmental conditions, our computational approach can help to choose a companion plant and appropriate farming practices. It also indicates how to estimate the robustness of IC to external perturbations. This approach, together with its results, can be viewed as an initial step toward "systems agriculture," which would ultimately develop systems of multiple plant grown together in appropriately designed and controlled settings.

PMID:39680765 | DOI:10.1073/pnas.2415315121

ACS Synth Biol. 2024 Dec 16. doi: 10.1021/acssynbio.4c00620. Online ahead of print.

ABSTRACT

Production of chemicals via metabolic engineering of microbes is becoming highly important for sustainable bioeconomy. Conventional metabolic engineering methodologies typically involve labor-intensive and time-consuming processes of iterative genetic modifications, which are inefficient in identifying new genetic targets for the construction of robust industrial strains on a large scale. To accelerate the creation of efficient microbial cell factories and enhance our insights into cellular metabolism, diverse large-scale genome libraries are emerging as powerful tools, which can be established through multiplex or parallel genome editing, gene expression regulation, and incorporation of evolutionary strategies. In this review, we discuss the latest advancements in the construction of genome-scale libraries as well as their applications within the domain of metabolic engineering. We also address the limitations of various techniques and provide insights into future prospects for the field.

PMID:39680725 | DOI:10.1021/acssynbio.4c00620

Development. 2024 Dec 16:dev.202703. doi: 10.1242/dev.202703. Online ahead of print.

ABSTRACT

Proneural genes are conserved drivers of neurogenesis across the animal kingdom. How their functions have adapted to guide human-specific neurodevelopmental features is poorly understood. Here, we mined transcriptomic data from human fetal cortices and generated from human embryonic stem cell (hESC)-derived cortical organoids (COs) to show that NEUROG1 and NEUROG2 are most highly expressed in basal neural progenitor cells, with pseudotime trajectory analyses indicating that NEUROG1-derived lineages predominate early and NEUROG2 lineages later. Using ChIP-qPCR, gene silencing and overexpression studies in COs, we show NEUROG2 is necessary and sufficient to directly transactivate known target genes (NEUROD1, EOMES, RND2). To identify new targets, we engineered NEUROG2-mCherry knock-in hESCs for CO generation. The mCherry-high CO cell transcriptome is enriched in extracellular matrix (ECM)-associated genes, and two genes associated with human-accelerated regions; PPP1R17 and FZD8. We show NEUROG2 binds COL1A1, COL3A1 and PPP1R17 regulatory elements and induces their ectopic expression in COs, although NEUROG2 is not required for this expression. Neurog2 similarly induces Col3a1 and Ppp1r17 in murine P19 cells. These data are consistent with a conservation of NEUROG2 function across mammalian species.

PMID:39680368 | DOI:10.1242/dev.202703

J Exp Bot. 2024 Dec 16:erae481. doi: 10.1093/jxb/erae481. Online ahead of print.

ABSTRACT

Sterols are produced via complex, multistep biosynthetic pathways involving similar enzymatic conversions in plants, animals and fungi, yielding a variety of sterol metabolites with slightly different chemical properties to exert diverse and specific functions. A tremendously diverse landscape of sterols, and sterol-derived compounds, can be found across the plant kingdom, determining a wide spectrum of functions. Resolving the underlying biosynthetic pathways is thus instrumental to understanding the function and use of these molecules. In only a few plants, sterol biosynthesis has been studied using mutants. In non-model species a pharmacological approach is required. However, this relies on only a few inhibitors. Here, we probed a collection of inhibitors of mammalian cholesterol biosynthesis to identify new inhibitors of plant sterol biosynthesis. We show that imidazole-type fungicides, bifonazole, clotrimazole and econazole inhibit the obtusifoliol 14α-demethylase CYP51 in plants. Moreover, we found that the selective estrogen receptor modulator, clomiphene, inhibits sterol biosynthesis in part by inhibiting the plant-specific cyclopropyl-cycloisomerase CPI1. These results demonstrate that rescreening of inhibitors animal sterol biosynthesis is an easy approach for identifying novel inhibitors of plant sterol biosynthesis. These molecules expand the toolkit for studying and manipulating sterol biosynthesis in the plant kingdom.

PMID:39680055 | DOI:10.1093/jxb/erae481

Biomacromolecules. 2024 Dec 16. doi: 10.1021/acs.biomac.4c01318. Online ahead of print.

ABSTRACT

Hyaluronic acid (HA) is a natural and biocompatible polysaccharide that is able to interact with CD44 receptors to regulate inflammation, fibrosis, and tissue reconstruction. It is a suitable chemical scaffold for drug delivery that can be functionalized with pharmacophores and/or vectorizable groups. The derivatization of HA is achieved to varying extents by reacting 1-amino-1-deoxy-lactitol via the carboxyl group to form amide linkages, giving rise to the grafted polymer, HYLACH. This retains the broad properties of HA, even though, as in most HA-grafted polymers, the detailed conformational effects of such substitutions, while crucial in the design or optimization of drug delivery systems, remain unknown. Here, the conformation, size, secondary structure, hydrogen bond network, and hydration features of lactosylated HA derivatives were evaluated by using multiple independent molecular dynamics simulations. This revealed subtle but nevertheless significant changes in the HA scaffold, establishing the density of grafting as the key parameter determining its properties.

PMID:39680036 | DOI:10.1021/acs.biomac.4c01318

J Chem Phys. 2024 Dec 21;161(23):234107. doi: 10.1063/5.0227527.

ABSTRACT

We show that the resolution-dependent loss of bimolecular reactions in spatiotemporal Reaction-Diffusion Master Equations (RDMEs) is in agreement with the mean-field Collins-Kimball (C-K) theory of diffusion-limited reaction kinetics. The RDME is a spatial generalization of the chemical master equation, which enables studying stochastic reaction dynamics in spatially heterogeneous systems. It uses a regular Cartesian grid to partition space into locally well-mixed reaction compartments and treats diffusion as a jump reaction between neighboring grid cells. As the chance for reactants to be in the same grid cell decreases for smaller cell widths, the RDME loses bimolecular reactions in finer grids. We show that for a single homo-bimolecular reaction, the mesh spacing can be interpreted as the reaction radius of a well-mixed C-K rate. Then, the bimolecular reaction loss is consistent with diffusion-limited kinetics in the mean-field steady state. In this interpretation, the constant in a bimolecular reaction propensity is no longer the macroscopic reaction rate but the rate of the ballistic C-K step. For the same grid resolution, different diffusion models in RDME, such as those based on finite differences and Gaussian jumps, represent different reaction radii.

PMID:39679507 | DOI:10.1063/5.0227527

Curr Zool. 2024 Mar 11;70(6):765-779. doi: 10.1093/cz/zoae009. eCollection 2024 Dec.

ABSTRACT

In social groups, competition for individual advantage is balanced with cooperation, for the collective benefit. Selection against aggression has favored cooperation and non-aggressive competitive strategies. Because social play is a behavioral system that fluctuates between cooperation and competition, selection against aggression might have especially influenced this behavior. African savannah elephants (Loxodonta africana) are a low aggressive species, therefore suitable to investigate this aspect. We collected all occurrences observational audio-video data on social play, aggression/threats, and affiliation on an African elephant colony housed in a 25-ha open space at Parque de la Naturaleza de Cabarceno (Cantabria, Spain) and composed of 4 family groups (3 immature males, 3 immature females, and 7 adult females) and 2 adult males. Anticipating the influence of reduced aggression, we found that social play decreased with age, persisting in adults, and that it was highest in males. Social play was associated with affiliation (informing cooperation). Indeed, individuals that were central in the social play network were also central in the affiliation network. For immature subjects, we found a correlation between social play and affiliation sociomatrices. However, such correlation was absent in adults and social play mostly occurred between families. Despite the limitations related to dealing with a small captive group, this study largely supports the idea that the features of social play in African savannah elephants may be related to low aggression. This investigation hints toward a non-purely cooperative use of play, possibly as a non-aggressive interaction that accommodates different levels of cooperation and competition.

PMID:39678814 | PMC:PMC11634687 | DOI:10.1093/cz/zoae009

iScience. 2024 May 30;27(6):110134. doi: 10.1016/j.isci.2024.110134. eCollection 2024 Jun 21.

ABSTRACT

Effective immune-cell responses depend on collective decision-making mediated by diffusible intercellular signaling proteins called cytokines. Here, we designed a three-dimensional spatiotemporal modeling framework and a precise finite-element simulation setup to systematically investigate the origin and consequences of spatially inhomogeneous cytokine distributions in lymph nodes. We found that such inhomogeneities are critical for effective paracrine signaling, and they do not arise by diffusion and uptake alone, but rather depend on properties of the cell population such as an all-or-none behavior of cytokine secreting cells. Furthermore, we assessed the regulatory properties of negative and positive feedback in combination with diffusion-limited signaling dynamics, and we derived statistical quantities to characterize the spatiotemporal signaling landscape in the context of specific tissue architectures. Overall, our simulations highlight the complex spatiotemporal dynamics imposed by cell-cell signaling with diffusible ligands, which entails a large potential for fine-tuned biological control especially if combined with feedback mechanisms.

PMID:39678490 | PMC:PMC11639737 | DOI:10.1016/j.isci.2024.110134

Front Genet. 2024 Nov 29;15:1460351. doi: 10.3389/fgene.2024.1460351. eCollection 2024.

ABSTRACT

INTRODUCTION: The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped.

METHODS: To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources.

RESULTS: Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments.

DISCUSSION: We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

PMID:39678381 | PMC:PMC11638175 | DOI:10.3389/fgene.2024.1460351

bioRxiv [Preprint]. 2024 Dec 5:2024.11.30.626166. doi: 10.1101/2024.11.30.626166.

ABSTRACT

In Diffuse Large B-cell Lymphoma (DLBCL), elevated anti-apoptotic BCL2-family proteins (e.g., MCL1, BCL2, BCLXL) and NF-κB subunits (RelA, RelB, cRel) confer poor prognosis. Heterogeneous expression, regulatory complexity, and redundancy offsetting the inhibition of individual proteins, complicate the assignment of targeted therapy. We combined flow cytometry 'fingerprinting', immunofluorescence imaging, and computational modeling to identify therapeutic vulnerabilities in DLBCL. The combined workflow predicted selective responses to BCL2 inhibition (venetoclax) and non-canonical NF-κB inhibition (Amgen16). Within the U2932 cell line we identified distinct resistance mechanisms to BCL2 inhibition in cellular sub-populations recapitulating intratumoral heterogeneity. Co-cultures with CD40L-expressing stromal cells, mimicking the tumor microenvironment (TME), induced resistance to BCL2 and BCLXL targeting BH3-mimetics via cell-type specific upregulation of BCLXL or MCL1. Computational models, validated experimentally, showed that basal NF-κB activation determined whether CD40 activation drove BH3-mimetic resistance through upregulation of RelB and BCLXL, or cRel and MCL1. High basal NF-κB activity could be overcome by inhibiting BTK to resensitize cells to BH3-mimetics in CD40L co-culture. Importantly, non-canonical NF-κB inhibition overcame heterogeneous compensatory BCL2 upregulation, restoring sensitivity to both BCL2-and BCLXL-targeting BH3-mimetics. Combined molecular fingerprinting and computational modelling provides a strategy for the precision use of BH3-mimetics and NF-κB inhibitors in DLBCL.

KEY POINTS: TME-mimicking co-culture provides resistance to BH3-mimetics through BCLXL, which can be overcome by inhibition of non-canonical NF-κB.Multidisciplinary profiling reveals how high NF-κB activity leads to crosstalk, and BH3-mimetic resistance counteracted by BTK inhibition.

PMID:39677808 | PMC:PMC11642794 | DOI:10.1101/2024.11.30.626166