White adipose tissue (WAT) is an essential regulator of energy storage and systemic metabolic homeostasis. Regulatory networks consisting of immune and structural cells are necessary to maintain WAT ...metabolism, which can become impaired during obesity in mammals. Using single-cell transcriptomics and flow cytometry, we unveil a large-scale comprehensive cellular census of the stromal vascular fraction of healthy lean and obese human WAT. We report new subsets and developmental trajectories of adipose-resident innate lymphoid cells, dendritic cells and monocyte-derived macrophage populations that accumulate in obese WAT. Analysis of cell-cell ligand-receptor interactions and obesity-enriched signaling pathways revealed a switch from immunoregulatory mechanisms in lean WAT to inflammatory networks in obese WAT. These results provide a detailed and unbiased cellular landscape of homeostatic and inflammatory circuits in healthy human WAT.
Antimicrobial resistance leads to failure of clinical antimicrobial therapy, and has raised urgent global public health concern. Humans can acquire antimicrobial resistance from drugs through the ...food chain or the environment (contaminated water, air, soil, or manure). While antimicrobials have been regular supplements in animal feed that maintain health and improve productivity of livestock, their over-use in feeding forage has led to a rise in antibacterial resistance. This review summarizes the current use of antimicrobials in livestock, the harmful effects of antimicrobial resistance, and the comprehensive combat measures.
•Antimicrobial abuse has become a serious problem.•Antimicrobial resistance poses a major threat to animal and human health.•Antibiotic growth promoters must be banned.
Targeting tumor-associated macrophages (TAMs) is a promising strategy to modify the immunosuppressive tumor microenvironment and improve cancer immunotherapy. Monoamine oxidase A (MAO-A) is an enzyme ...best known for its function in the brain; small molecule MAO inhibitors (MAOIs) are clinically used for treating neurological disorders. Here we observe MAO-A induction in mouse and human TAMs. MAO-A-deficient mice exhibit decreased TAM immunosuppressive functions corresponding with enhanced antitumor immunity. MAOI treatment induces TAM reprogramming and suppresses tumor growth in preclinical mouse syngeneic and human xenograft tumor models. Combining MAOI and anti-PD-1 treatments results in synergistic tumor suppression. Clinical data correlation studies associate high intratumoral MAOA expression with poor patient survival in a broad range of cancers. We further demonstrate that MAO-A promotes TAM immunosuppressive polarization via upregulating oxidative stress. Together, these data identify MAO-A as a critical regulator of TAMs and support repurposing MAOIs for TAM reprogramming to improve cancer immunotherapy.
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•Spectral properties and Cu-binding properties of DOM collected from the upper lake and lower lake in Nansi Lake were studied.•Humic-/fulvic-like substances were the main substance of ...DOM collected from Nansi Lake.•Protein-like components exhibited higher Cu (II) binding abilities than humic-/fulvic-like ones.•Interactions of Cu2+ with DOM were probably affected by submerged plants and the water conservancy projects.
Interaction between dissolved organic matter (DOM) and heavy metals have been widely studied, and the differences in DOM properties have a great impact on the capacity of DOM-metals binding. In this study, the samples were collected from the upper lake and lower lake in Nansi Lake, respectively. According to the ratio of the fluorescence intensity of component to the total fluorescence intensity (%Fmax) in the two areas, obvious differences were found in the properties of DOM. The content of humic-like substances showed a decreasing trend from the north to south in Nansi Lake. On this basis, samples from north and south ends of Nansi Lake were selected for fluorescence titration. All components were quenched with the increasing of Cu2+ addition. Combining the results of Synchronous fluorescence (SF) spectra with two-dimensional correlation spectroscopy (2D-COS), fluorescent quenching near 275 nm was quicker than the changes that occurred at the wavelength that after 275 nm, which suggested that the complexation occurred firstly for protein-like components as compared with humic-like components. The modified Stern-Volmer model suggested that protein-like components had larger effective quenching constants (logKa = 3.47 ± 0.13 for component C5 in the upper lake and logKa = 3.57 ± 0.19 for component C4 in the lower lake) than humic-like components and it is not affected by the region, indicating that protein-like substances might have a higher metal binding potential than humic-like substances in Nansi Lake. The binding constants and the binding sites suggested that humic-like components also had a nonnegligible binding potential in Nansi Lake although the protein-like components revealed a stronger binding ability in fluorescence quenching.
High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable characterization of complex biological samples by increasing the number of cells that can be profiled contemporaneously. ...Nevertheless, these approaches recover less information per cell than low-throughput strategies. To accurately report the expression of key phenotypic features of cells, scRNA-seq platforms are needed that are both high fidelity and high throughput. To address this need, we created Seq-Well S3 (“Second-Strand Synthesis”), a massively parallel scRNA-seq protocol that uses a randomly primed second-strand synthesis to recover complementary DNA (cDNA) molecules that were successfully reverse transcribed but to which a second oligonucleotide handle, necessary for subsequent whole transcriptome amplification, was not appended due to inefficient template switching. Seq-Well S3 increased the efficiency of transcript capture and gene detection compared with that of previous iterations by up to 10- and 5-fold, respectively. We used Seq-Well S3 to chart the transcriptional landscape of five human inflammatory skin diseases, thus providing a resource for the further study of human skin inflammation.
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•Seq-Well S3 uses second-strand synthesis to improve transcript capture•Seq-Well S3 was benchmarked against a best-in-class commercial platform•Seq-Well S3 was applied to profile inflammatory cell states in skin diseases•Analysis of skin inflammation uncovered unique and conserved cellular phenotypes
Hughes et al. report the development of a technique for high-throughput single-cell RNA-sequencing, “Seq-Well S3,” that enables increased sensitivity and improved detection of genes including transcription factors, cytokines, and cytokine receptors. Using Seq-Well S3, the authors define inflammatory cell states across multiple skin diseases.
The ontogeny of human haematopoietic stem cells (HSCs) is poorly defined owing to the inability to identify HSCs as they emerge and mature at different haematopoietic sites
. Here we created a ...single-cell transcriptome map of human haematopoietic tissues from the first trimester to birth and found that the HSC signature RUNX1
HOXA9
MLLT3
MECOM
HLF
SPINK2
distinguishes HSCs from progenitors throughout gestation. In addition to the aorta-gonad-mesonephros region, nascent HSCs populated the placenta and yolk sac before colonizing the liver at 6 weeks. A comparison of HSCs at different maturation stages revealed the establishment of HSC transcription factor machinery after the emergence of HSCs, whereas their surface phenotype evolved throughout development. The HSC transition to the liver marked a molecular shift evidenced by suppression of surface antigens reflecting nascent HSC identity, and acquisition of the HSC maturity markers CD133 (encoded by PROM1) and HLA-DR. HSC origin was tracked to ALDH1A1
KCNK17
haemogenic endothelial cells, which arose from an IL33
ALDH1A1
arterial endothelial subset termed pre-haemogenic endothelial cells. Using spatial transcriptomics and immunofluorescence, we visualized this process in ventrally located intra-aortic haematopoietic clusters. The in vivo map of human HSC ontogeny validated the generation of aorta-gonad-mesonephros-like definitive haematopoietic stem and progenitor cells from human pluripotent stem cells, and serves as a guide to improve their maturation to functional HSCs.
Scar tissue size following myocardial infarction is an independent predictor of cardiovascular outcomes, yet little is known about factors regulating scar size. We demonstrate that collagen V, a ...minor constituent of heart scars, regulates the size of heart scars after ischemic injury. Depletion of collagen V led to a paradoxical increase in post-infarction scar size with worsening of heart function. A systems genetics approach across 100 in-bred strains of mice demonstrated that collagen V is a critical driver of postinjury heart function. We show that collagen V deficiency alters the mechanical properties of scar tissue, and altered reciprocal feedback between matrix and cells induces expression of mechanosensitive integrins that drive fibroblast activation and increase scar size. Cilengitide, an inhibitor of specific integrins, rescues the phenotype of increased post-injury scarring in collagen-V-deficient mice. These observations demonstrate that collagen V regulates scar size in an integrin-dependent manner.
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•Collagen V deficiency increases scar size after acute heart injury•Mechanical properties of scars are altered with Col V deficiency•Altered mechanosensitive cues augment myofibroblast formation in scar•Inhibition of specific integrins rescues increased scarring in Col-V-deficient states
Scar tissue size following heart injury is a predictor of cardiovascular outcomes. Yokota et al. find that a specific collagen, type V, plays a paradoxical role in limiting scar size by altering the mechanical properties of developing scar tissue.
Nansi Lake is the largest lake along the eastern route of China’s South-to-North Water Diversion Project (SNWDP). It is divided into the upper lake and the lower lake by a dam. By using UV-Vis ...spectroscopy, synchronous fluorescence (SF) spectroscopy, excitation-emission matrix and parallel factor analysis (EEM-PARAFAC), spatial, and temporal differences in the properties of dissolved organic matter (DOM) were found in the 2 areas of Nansi Lake under different hydrological conditions. A total of 5 fluorescence components were obtained by EEM-PARAFAC, which included 3 humic-like components (C1–C3) and 2 protein-like components (C4 and C5). On the spatial scale, the fluorescence intensities (
F
max
) of humic-like substances and the ratio of the fluorescence intensity of humic-like components to the total fluorescence intensity (%
F
max
) and degree of humification (HIX) in the upper lake were higher than those in the lower lake. This indicated the strong contributions of terrestrial sources to the upper lake, while DOM properties in the lower lake were more endogenous than those in the upper lake. On the temporal scale, protein-like substances played a more important role in DOM properties in April (
F
max
=0.72±0.03 in the upper lake and 1.84±0.13 in the lower lake) and July (
F
max
=1.10±0.05 in the upper lake and 1.49±0.04 in the lower lake) than in October. This result might be related to the water transfer of the eastern route of the SNWDP and to the death of submerged plants. However, the contents of humic-like substances (ranging from 55.61±1.23% to 66.56±0.58% for the upper lake and 29.98±1.56% to 61.98±0.99% for the lower lake) and degree of humification (from 2.23±0.06 to 3.10±0.05 for the upper lake and 1.06±0.05 to 2.62±0.08 for the lower lake) in Nansi Lake showed an increasing trend from April to October. In addition, significant correlations and good linear relationships between humic-like components,
a
254
, and DOC in the 3 months reflected the continuous contribution of humic-like substances to DOM properties in Nansi Lake. Rapid changes in the fluorescence signal were largely dependent on changes in water quality. The fluorescence signal could be a tool for the management of water quality in Nansi Lake.
Abstract
Motivation
Cell type identification is one of the major goals in single cell RNA sequencing (scRNA-seq). Current methods for assigning cell types typically involve the use of unsupervised ...clustering, the identification of signature genes in each cluster, followed by a manual lookup of these genes in the literature and databases to assign cell types. However, there are several limitations associated with these approaches, such as unwanted sources of variation that influence clustering and a lack of canonical markers for certain cell types. Here, we present ACTINN (Automated Cell Type Identification using Neural Networks), which employs a neural network with three hidden layers, trains on datasets with predefined cell types and predicts cell types for other datasets based on the trained parameters.
Results
We trained the neural network on a mouse cell type atlas (Tabula Muris Atlas) and a human immune cell dataset, and used it to predict cell types for mouse leukocytes, human PBMCs and human T cell sub types. The results showed that our neural network is fast and accurate, and should therefore be a useful tool to complement existing scRNA-seq pipelines.
Availability and implementation
The codes and datasets are available at https://figshare.com/articles/ACTINN/8967116. Tutorial is available at https://github.com/mafeiyang/ACTINN. All codes are implemented in python.
Supplementary information
Supplementary data are available at Bioinformatics online.
Natural killer (NK) cells are innate lymphocytes that possess traits of adaptive immunity, such as memory formation. However, the molecular mechanisms by which NK cells persist to form memory cells ...are not well understood. Using single-cell RNA sequencing, we identified two distinct effector NK cell (NK
) populations following mouse cytomegalovirus infection. Ly6C
memory precursor (MP) NK cells showed enhanced survival during the contraction phase in a Bcl2-dependent manner, and differentiated into Ly6C
memory NK cells. MP NK cells exhibited distinct transcriptional and epigenetic signatures compared with Ly6C
NK
cells, with a core epigenetic signature shared with MP CD8
T cells enriched in ETS1 and Fli1 DNA-binding motifs. Fli1 was induced by STAT5 signaling ex vivo, and increased levels of the pro-apoptotic factor Bim in early effector NK cells following viral infection. These results suggest that a NK cell-intrinsic checkpoint controlled by the transcription factor Fli1 limits MP NK formation by regulating early effector NK cell fitness during viral infection.
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