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1.
Science ; 376(6594): eabl4896, 2022 05 13.
Article in English | MEDLINE | ID: mdl-35549404

ABSTRACT

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.


Subject(s)
Atlases as Topic , Cells , Organ Specificity , RNA Splicing , Single-Cell Analysis , Transcriptome , B-Lymphocytes/metabolism , Cells/metabolism , Humans , Organ Specificity/genetics , T-Lymphocytes/metabolism
2.
Curr Opin Chem Biol ; 68: 102151, 2022 06.
Article in English | MEDLINE | ID: mdl-35483127

ABSTRACT

Electrogenetics, the combination of electronics and genetics, is an emerging field of mammalian synthetic biology in which electrostimulation is used to remotely program user-designed genetic elements within designer cells to generate desired outputs. Here, we describe recent advances in electro-induced therapeutic gene expression and therapeutic protein secretion in engineered mammalian cells. We also review available tools and strategies to engineer electro-sensitive therapeutic designer cells that are able to sense electrical pulses and produce appropriate clinically relevant outputs in response. We highlight current limitations facing mammalian electrogenetics and suggest potential future directions for research.


Subject(s)
Cell Engineering , Cells , Electric Stimulation , Genetics , Mammals , Synthetic Biology , Animals , Cell Engineering/methods , Cell Physiological Phenomena/genetics , Cells/metabolism , Electric Stimulation/methods , Electric Stimulation Therapy , Electronics , Gene Expression Regulation , Mammals/genetics , Protein Biosynthesis , Synthetic Biology/methods , Telemetry
3.
Cell ; 185(2): 345-360.e28, 2022 01 20.
Article in English | MEDLINE | ID: mdl-35063075

ABSTRACT

We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.


Subject(s)
Cells/cytology , Computer Simulation , Adenosine Triphosphate/metabolism , Cell Cycle/genetics , Cell Proliferation/genetics , Cells/metabolism , DNA Replication/genetics , Gene Expression Regulation , Imaging, Three-Dimensional , Kinetics , Lipids/chemistry , Metabolic Networks and Pathways , Metabolome , Molecular Sequence Annotation , Nucleotides/metabolism , Thermodynamics , Time Factors
4.
Nat Commun ; 13(1): 385, 2022 01 19.
Article in English | MEDLINE | ID: mdl-35046414

ABSTRACT

Mapping cell types across a tissue is a central concern of spatial biology, but cell type abundance is difficult to extract from spatial gene expression data. We introduce SpatialDecon, an algorithm for quantifying cell populations defined by single cell sequencing within the regions of spatial gene expression studies. SpatialDecon incorporates several advancements in gene expression deconvolution. We propose an algorithm harnessing log-normal regression and modelling background, outperforming classical least-squares methods. We compile cell profile matrices for 75 tissue types. We identify genes whose minimal expression by cancer cells makes them suitable for immune deconvolution in tumors. Using lung tumors, we create a dataset for benchmarking deconvolution methods against marker proteins. SpatialDecon is a simple and flexible tool for mapping cell types in spatial gene expression studies. It obtains cell abundance estimates that are spatially resolved, granular, and paired with highly multiplexed gene expression data.


Subject(s)
Algorithms , Cells/metabolism , Transcriptome/genetics , Cell Line, Tumor , HEK293 Cells , Humans , Least-Squares Analysis , Neoplasms/genetics , Neoplasms/immunology , Regression Analysis , Tumor Microenvironment/genetics
6.
Pak J Biol Sci ; 24(11): 1138-1143, 2021 Jan.
Article in English | MEDLINE | ID: mdl-34842385

ABSTRACT

<b>Background and Objective:</b> The composition of the waste consists mostly of plant biomass. Cellulose is the largest component of plant biomass and cellulolytic bacteria are needed to degrade it. This study aimed to determine enzyme activity possessed by bacterial isolates from Biological Education and Research Forest floor Andalas University. <b>Materials and Methods:</b> The isolation stage was carried out with NA (Nutrient agar) medium, Screening with CMC (Carboxymethyl Cellulose) medium with congo red dye and enzyme activity testing was carried out using the Nelson-Somogyi method. <b>Results:</b> We found 16 bacterial isolates obtained from Biological Education and Research Forest Floor Andalas University, 10 of them were positive for cellulolytic bacteria with the highest cellulolytic index value of 2.59 on FFB 2 isolates. <b>Conclusion:</b> The bacterial isolate with the best enzyme activity value was FFB 2 isolate 0.166 U mL<sup>1</sup> for 72 hrs.


Subject(s)
Bacteria/enzymology , Cells/microbiology , Bacteria/metabolism , Cells/metabolism , Forests , Indonesia
7.
Nat Commun ; 12(1): 6778, 2021 11 26.
Article in English | MEDLINE | ID: mdl-34836951

ABSTRACT

Protein turnover is critical to cellular physiology as well as to the growth and maintenance of tissues. The unique synthesis and degradation rates of each protein help to define tissue phenotype, and knowledge of tissue- and protein-specific half-lives is directly relevant to protein-related drug development as well as the administration of medical therapies. Using stable isotope labeling and mass spectrometry, we determine the in vivo turnover rates of thousands of proteins-including those of the extracellular matrix-in a set of biologically important mouse tissues. We additionally develop a data visualization platform, named ApplE Turnover, that enables facile searching for any protein of interest in a tissue of interest and then displays its half-life, confidence interval, and supporting measurements. This extensive dataset and the corresponding visualization software provide a reference to guide future studies of mammalian protein turnover in response to physiologic perturbation, disease, or therapeutic intervention.


Subject(s)
Cells/metabolism , Extracellular Matrix/metabolism , Proteins/metabolism , Proteomics/methods , Animals , Isotope Labeling/methods , Mass Spectrometry/methods , Mice , Proteome/metabolism , Software
8.
Osteoarthritis Cartilage ; 30(2): 280-290, 2022 02.
Article in English | MEDLINE | ID: mdl-34826571

ABSTRACT

OBJECTIVE: Although cartilage degeneration and invasion of the subchondral bone plate in entheseal lesion has been considered to consequently lead bony ankylosis in ankylosing spondylitis (AS), no evident mechanisms are known. DESIGN: To identify histopathological and physiological changes in enthesitis-related ankylosis in AS, we performed molecular characterization of transcription factors and surface markers, and transcriptome analysis with human tissues. Entheseal tissue containing subchondral bone was obtained from the facet joints of 9 patients with AS and 10 disease controls, and assessed by using differential staining techniques. Enthesis cells were isolated, characterized, stimulated with TNF and/or IL-17A, and analysed by cell-based experimental tools. RESULTS: We found diffusely distributed granular tissue and cartilage in the subchondral bone in AS. Co-expression of SOX9, a specific transcription factor in cartilage, and matrix metalloproteinase 13 (MMP13) was found in the granular tissues within the subchondral bone from AS patients. Intriguingly, SOX9 expression was significantly higher in AS enthesis cells than controls and correlated with TNFR1 and IL-17RA expressions, which is important for high reactivity to TNF and IL-17A cytokines. Co-stimulation by TNF and IL-17A resulted in accelerated mineralization/calcification features, and increased OCN expression in AS enthesis cells. Furthermore, SOX9 overexpression in enthesis leads to promoting mineralization feature by TNF and IL-17A stimuli. Finally, OCN expression is elevated in the destructive enthesis of advanced AS. CONCLUSION: These findings provide insight into the links between inflammation and the mineralization of entheseal tissue as the initiation of spinal ankylosis, emphasizing the importance of SOX9+ enthesis cells.


Subject(s)
Ankylosis/pathology , SOX9 Transcription Factor , Spinal Diseases/pathology , Spondylitis, Ankylosing/pathology , Adult , Cells/metabolism , Female , Humans , Ligaments, Articular/cytology , Male , Middle Aged , SOX9 Transcription Factor/biosynthesis , Tendons/cytology
9.
Nature ; 599(7886): 684-691, 2021 11.
Article in English | MEDLINE | ID: mdl-34789882

ABSTRACT

The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.


Subject(s)
Brain/cytology , Cells/classification , Chromatin Assembly and Disassembly , Chromatin/chemistry , Chromatin/genetics , Genes , Molecular Conformation , Animals , Binding Sites , Cells/metabolism , Chromatin/metabolism , Gene Expression Regulation , Male , Mice , Multigene Family/genetics , Neurons/classification , Neurons/metabolism , Nucleic Acid Denaturation , Transcription Factors/metabolism
11.
Nat Cell Biol ; 23(11): 1129-1135, 2021 11.
Article in English | MEDLINE | ID: mdl-34750578

ABSTRACT

Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body while at the same time raising the need to formalize this new knowledge. Here, we discuss current efforts to harmonize and integrate different sources of annotations of cell types and states into a reference cell ontology. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains.


Subject(s)
Atlases as Topic , Cell Biology , Cell Lineage , Cells/classification , Single-Cell Analysis , Biological Ontologies , Biomarkers/metabolism , Cells/metabolism , Cells/pathology , Data Mining , Disease , Gene Ontology , Genomics , High-Throughput Nucleotide Sequencing , Humans , Phenotype , Systems Integration , Transcriptome
12.
Nat Cell Biol ; 23(11): 1117-1128, 2021 11.
Article in English | MEDLINE | ID: mdl-34750582

ABSTRACT

The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked parts of the HRA: (1) three-dimensional representations of anatomy that are linked to (2) tables that name and interlink major anatomical structures, cell types, plus biomarkers (ASCT+B). We discuss four examples that demonstrate the practical utility of the HRA.


Subject(s)
Atlases as Topic , Cell Biology , Cell Lineage , Cells/classification , Single-Cell Analysis , Biomarkers/metabolism , Cells/metabolism , Cells/pathology , Computer Graphics , Disease , Genomics , High-Throughput Nucleotide Sequencing , Humans , Phenotype , Transcriptome
13.
Phys Rev Lett ; 127(17): 178101, 2021 Oct 22.
Article in English | MEDLINE | ID: mdl-34739268

ABSTRACT

The movement of single kinesin molecules was observed while applying noisy external forces that mimic intracellular active fluctuations. We found kinesin accelerates under noise, especially when a large hindering load is added. The behavior quantitatively conformed to a theoretical model that describes the kinesin movement with simple two-state reactions. The universality of the kinetic theory suggests that intracellular enzymes share a similar noise-induced acceleration mechanism, i.e., active fluctuations in cells are not just noise but are utilized to promote various physiological processes.


Subject(s)
Acceleration , Cells/metabolism , /metabolism , Cells/enzymology , Kinetics , Models, Biological
14.
Cells ; 10(10)2021 10 09.
Article in English | MEDLINE | ID: mdl-34685688

ABSTRACT

The idea of remote magnetic guiding is developed from the underlying physics of a concept that allows for bijective force generation over the inner volume of magnet systems. This concept can equally be implemented by electro- or permanent magnets. Here, permanent magnets are in the focus because they offer many advantages. The equations of magnetic fields and forces as well as velocities are derived in detail and physical limits are discussed. The special hydrodynamics of nanoparticle dispersions under these circumstances is reviewed and related to technical constraints. The possibility of 3D guiding and magnetic imaging techniques are discussed. Finally, the first results in guiding macroscopic objects, superparamagnetic nanoparticles, and cells with incorporated nanoparticles are presented. The constructed magnet systems allow for orientation, movement, and acceleration of magnetic objects and, in principle, can be scaled up to human size.


Subject(s)
Cells/metabolism , Magnetic Phenomena , Magnets , Nanoparticles/chemistry , Animals , Humans , Imaging, Three-Dimensional , Magnetic Fields
15.
Cell Metab ; 33(10): 1895, 2021 10 05.
Article in English | MEDLINE | ID: mdl-34614402

Subject(s)
Cells , Cells/metabolism , China , Humans
16.
Biomolecules ; 11(9)2021 09 09.
Article in English | MEDLINE | ID: mdl-34572547

ABSTRACT

The gene encoding the High Mobility Group A1 (HMGA1) chromatin remodeling protein is upregulated in diverse cancers where high levels portend adverse clinical outcomes. Until recently, HMGA1 was assumed to be a nuclear protein exerting its role in cancer by transcriptionally modulating gene expression and downstream signaling pathways. However, the discovery of an extracellular HMGA1-RAGE autocrine loop in invasive triple-negative breast cancer (TNBC) cell lines implicates HMGA1 as a "moonlighting protein" with different functions depending upon cellular location. Here, we review the role of HMGA1, not only as a chromatin regulator in cancer and stem cells, but also as a potential secreted factor that drives tumor progression. Prior work found that HMGA1 is secreted from TNBC cell lines where it signals through the receptor for advanced glycation end products (RAGE) to foster phenotypes involved in tumor invasion and metastatic progression. Studies in primary TNBC tumors also suggest that HMGA1 secretion associates with distant metastasis in TNBC. Given the therapeutic potential to target extracellular proteins, further work to confirm this role in other contexts is warranted. Indeed, crosstalk between nuclear and secreted HMGA1 could change our understanding of tumor development and reveal novel therapeutic opportunities relevant to diverse human cancers overexpressing HMGA1.


Subject(s)
Cells/metabolism , HMGA1a Protein/metabolism , Animals , Cell Compartmentation , Humans , Models, Biological , Neoplasms/metabolism , Oncogenes
17.
Nature ; 597(7877): 533-538, 2021 09.
Article in English | MEDLINE | ID: mdl-34497420

ABSTRACT

Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. However, the systematic mapping of the interactions between drugs and bacteria has only started recently1 and the main underlying mechanism proposed is the chemical transformation of drugs by microorganisms (biotransformation). Here we investigated the depletion of 15 structurally diverse drugs by 25 representative strains of gut bacteria. This revealed 70 bacteria-drug interactions, 29 of which had not to our knowledge been reported before. Over half of the new interactions can be ascribed to bioaccumulation; that is, bacteria storing the drug intracellularly without chemically modifying it, and in most cases without the growth of the bacteria being affected. As a case in point, we studied the molecular basis of bioaccumulation of the widely used antidepressant duloxetine by using click chemistry, thermal proteome profiling and metabolomics. We find that duloxetine binds to several metabolic enzymes and changes the metabolite secretion of the respective bacteria. When tested in a defined microbial community of accumulators and non-accumulators, duloxetine markedly altered the composition of the community through metabolic cross-feeding. We further validated our findings in an animal model, showing that bioaccumulating bacteria attenuate the behavioural response of Caenorhabditis elegans to duloxetine. Together, our results show that bioaccumulation by gut bacteria may be a common mechanism that alters drug availability and bacterial metabolism, with implications for microbiota composition, pharmacokinetics, side effects and drug responses, probably in an individual manner.


Subject(s)
Bacteria/metabolism , Bioaccumulation , Duloxetine Hydrochloride/metabolism , Gastrointestinal Microbiome/physiology , Animals , Antidepressive Agents/metabolism , Antidepressive Agents/pharmacokinetics , Caenorhabditis elegans/metabolism , Cells/metabolism , Click Chemistry , Duloxetine Hydrochloride/adverse effects , Duloxetine Hydrochloride/pharmacokinetics , Humans , Metabolomics , Models, Animal , Proteomics , Reproducibility of Results
18.
Molecules ; 26(16)2021 Aug 04.
Article in English | MEDLINE | ID: mdl-34443297

ABSTRACT

The potential of nanomaterials use is huge, especially in fields such as medicine or industry. Due to widespread use of nanomaterials, their cytotoxicity and involvement in cellular pathways ought to be evaluated in detail. Nanomaterials can induce the production of a number of substances in cells, including reactive oxygen species (ROS), participating in physiological and pathological cellular processes. These highly reactive substances include: superoxide, singlet oxygen, hydroxyl radical, and hydrogen peroxide. For overall assessment, there are a number of fluorescent probes in particular that are very specific and selective for given ROS. In addition, due to the involvement of ROS in a number of cellular signaling pathways, understanding the principle of ROS production induced by nanomaterials is very important. For defense, the cells have a number of reparative and especially antioxidant mechanisms. One of the most potent antioxidants is a tripeptide glutathione. Thus, the glutathione depletion can be a characteristic manifestation of harmful effects caused by the prooxidative-acting of nanomaterials in cells. For these reasons, here we would like to provide a review on the current knowledge of ROS-mediated cellular nanotoxicity manifesting as glutathione depletion, including an overview of approaches for the detection of ROS levels in cells.


Subject(s)
Cells/metabolism , Glutathione/metabolism , Nanostructures/toxicity , Oxidative Stress/drug effects , Reactive Oxygen Species/metabolism , Animals , Cells/drug effects , Humans , Signal Transduction/drug effects
19.
Molecules ; 26(16)2021 Aug 07.
Article in English | MEDLINE | ID: mdl-34443378

ABSTRACT

Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.


Subject(s)
Biocatalysis , Cells/metabolism , Enzymes/isolation & purification , Ionic Liquids/chemistry , Solubility
20.
Molecules ; 26(16)2021 Aug 11.
Article in English | MEDLINE | ID: mdl-34443459

ABSTRACT

Antioxidants remain interesting molecules of choice for suppression of the toxic effects of free radicals in foods and human systems. The current practice involves the use of mainly synthetic molecules as potent antioxidant agents. However, due to the potential negative impact on human health, there is an intensive effort within the research community to develop natural alternatives with similar antioxidant efficacy but without the negative side effects of synthetic molecules. Still, the successful development of new molecules depends on the use of reliable chemical or cell culture assays to screen antioxidant properties. Chemical antioxidant assays include the determination of scavenging ability against free radicals such as DPPH, superoxide anion radicals, hydroxyl radicals, hydrogen peroxide, and nitric oxide. Other antioxidant tests include the ability of compounds to bind and sequester prooxidant metal cations, reduce ferric iron, and attenuate the rate of lipid oxidation. Ex vivo tests utilize cell cultures to confirm entry of the molecules into cells and the ability to quench synthetic intracellular free radicals or to stimulate the increased biosynthesis of endogenous antioxidants. In order to assist researchers in their choice of antioxidant evaluation methods, this review presents background scientific information on some of the most commonly used antioxidant assays with a comparative discussion of the relevance of published literature data to food science and human nutrition applications.


Subject(s)
Antioxidants/metabolism , Biological Assay/methods , Cells/metabolism , Antioxidants/chemistry , Cell Membrane/metabolism , Humans , Lipid Peroxidation , Reactive Oxygen Species/metabolism
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