Benchmarking automated cell type annotation tools for single-cell ATAC-seq data

As single-cell chromatin accessibility profiling methods advance, scATAC-seq has become ever more important in the study of candidate regulatory genomic regions and their roles underlying developmental, evolutionary, and disease processes. At the same time, cell type annotation is critical in understanding the cellular composition of complex tissues and identifying potential novel cell types. However, most existing methods that can perform automated cell type annotation are designed to transfer labels from an annotated scRNA-seq data set to another scRNA-seq data set, and it is not clear whether these methods are adaptable to annotate scATAC-seq data. Several methods have been recently proposed for label transfer from scRNA-seq data to scATAC-seq data, but there is a lack of benchmarking study on the performance of these methods. Here, we evaluated the performance of five scATAC-seq annotation methods on both their classification accuracy and scalability using publicly available single-cell datasets from mouse and human tissues including brain, lung, kidney, PBMC, and BMMC. Using the BMMC data as basis, we further investigated the performance of these methods across different data sizes, mislabeling rates, sequencing depths and the number of cell types unique to scATAC-seq. Bridge integration, which is the only method that requires additional multimodal data and does not need gene activity calculation, was overall the best method and robust to changes in data size, mislabeling rate and sequencing depth. Conos was the most time and memory efficient method but performed the worst in terms of prediction accuracy. scJoint tended to assign cells to similar cell types and performed relatively poorly for complex datasets with deep annotations but performed better for datasets only with major label annotations. The performance of scGCN and Seurat v3 was moderate, but scGCN was the most time-consuming method and had the most similar performance to random classifiers for cell types unique to scATAC-seq

Identification of 27 abnormalities from multi-lead ECG signals: An ensembled Se-ResNet framework with Sign Loss function

Cardiovascular disease is a major threat to health and one of the primary causes of death globally. The 12-lead ECG is a cheap and commonly accessible tool to identify cardiac abnormalities. Early and accurate diagnosis will allow early treatment and intervention to prevent severe complications of cardiovascular disease. In the PhysioNet/Computing in Cardiology Challenge 2020, our objective is to develop an algorithm that automatically identifies 27 ECG abnormalities from 12-lead ECG recordings

PtdIns (3,4,5) P3 Recruitment of Myo10 Is Essential for Axon Development

Myosin X (Myo10) with pleckstrin homology (PH) domains is a motor protein acting in filopodium initiation and extension. However, its potential role has not been fully understood, especially in neuronal development. In the present study the preferential accumulation of Myo10 in axon tips has been revealed in primary culture of hippocampal neurons with the aid of immunofluorescence from anti-Myo10 antibody in combination with anti-Tuj1 antibody as specific marker. Knocking down Myo10 gene transcription impaired outgrowth of axon with loss of Tau-1-positive phenotype. Interestingly, inhibition of actin polymerization by cytochalasin D rescued the defect of axon outgrowth. Furthermore, ectopic expression of Myo10 with enhanced green fluorescence protein (EGFP) labeled Myo10 mutants induced multiple axon-like neurites in a motor-independent way. Mechanism studies demonstrated that the recruitment of Myo10 through its PH domain to phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5) P3) was essential for axon formation. In addition, in vivo studies confirmed that Myo10 was required for neuronal morphological transition during radial neuronal migration in the developmental neocortex

Icariin Protects Bone Marrow Mesenchymal Stem Cells Against Iron Overload Induced Dysfunction Through Mitochondrial Fusion and Fission, PI3K/AKT/mTOR and MAPK Pathways

Iron overload has been reported to contribute to bone marrow mesenchymal stem cells (BMSCs) damage, but the precise mechanism still remains elusive. Icariin, a major bioactive monomer belonging to flavonoid glucosides isolated from Herba Epimedii, has been shown to protect cells from oxidative stress induced apoptosis. The aim of this study was to investigate whether icariin protected against iron overload induced dysfunction of BMSCs and its underlying mechanism. In this study, we found that iron overload induced by 100 μM ferric ammonium citrate (FAC) caused apoptosis of BMSCs, promoted cleaved caspase-3 and BAX protein expressions while inhibited Bcl-2 protein expression, which effects were significantly attenuated by icariin treatment. In addition, iron overload induced significant depolarization of mitochondrial membrane potential (MMP), reactive oxygen species (ROS) generation and inhibition of mitochondrial fusion/fission, which effects were also attenuated by icariin treatment. Meanwhile, we found that iron overload induced by 100 μM FAC significantly inhibited mitochondrial fission protein FIS1 and fusion protein MFN2 expressions, inhibited DRP1 and Cytochrome C protein translocation from the cytoplasm to mitochondria. Icariin at concentration of 1 μM was able to promote mitochondrial fission protein FIS1 and fusion protein MFN2 expressions, and increase DRP1 and cytochrome C protein translocation from the cytoplasm to mitochondria. Further, osteogenic differentiation and proliferation of BMSCs was significantly inhibited by iron overload, but icariin treatment rescued both osteogenic differentiation and proliferation of BMSCs. Further studies showed that icariin attenuated iron overload induced inactivation of the PI3K/AKT/mTOR pathway and activation of the ERK1/2 and JNK pathways. In summary, our study indicated that icariin was able to protect against iron overload induced dysfunction of BMSCs. These effects were potentially related to the modulation of mitochondrial fusion and fission, activation of the PI3K/AKT/mTOR pathway and inhibition of ERK1/2 and JNK pathways

An immunological electrospun scaffold for tumor cell killing and healthy tissue regeneration

Antibody-based cancer immune therapy has attracted lots of research interest in recent years; however, it is greatly limited by the easy distribution and burst release of antibodies. In addition, after the clearance of the tissue, healthy tissue regeneration is another challenge for cancer treatment. Herein, we have developed a specific immunological tissue engineering scaffold using the agonistic mouse anti-human CD40 antibody (CD40mAb) incorporated into poly(l-lactide) (PLLA) electrospun fibers through the dopamine (PDA) motif (PLLA-PDA-CD40mAb). CD40mAb is successfully incorporated onto the surface of the electrospun fibrous scaffold, which is proved by immunofluorescence staining, and the PLLA-PDA-CD40mAb scaffold has an anti-tumor effect by locally releasing CD40mAb. Therefore, this immunological electrospun scaffold has very good potential to be developed as a powerful tool for localized tumor treatment, and this is the first to be reported in this area.Peer reviewe

Therapeutic potential of garlic chive-derived vesicle-like nanoparticles in NLRP3 inflammasome-mediated inflammatory diseases

Aberrant activation of the nucleotide-binding domain and leucine-rich repeat related (NLR) family, pyrin domain containing 3 (NLRP3) inflammasome drives the development of many complex inflammatory diseases, such as obesity, Alzheimer\u27s disease, and atherosclerosis. However, no medications specifically targeting the NLRP3 inflammasome have become clinically available. Therefore, we aim to identify new inhibitors of the NLRP3 inflammasome in this study. Methods: Vesicle-like nanoparticles (VLNs) were extracted from garlic chives and other Allium vegetables and their effects on the NLRP3 inflammasome were evaluated in primary macrophages. After garlic chive-derived VLNs (GC-VLNs) were found to exhibit potent anti-NLRP3 inflammasome activity in cell culture, such function was further assessed in a murine acute liver injury disease model, as well as in diet-induced obesity. Finally, GC-VLNs were subjected to omics analysis to identify the active components with anti-NLRP3 inflammasome function. Results: GC-VLNs are membrane-enclosed nanoparticles containing lipids, proteins, and RNAs. They dose-dependently inhibit pathways downstream of NLRP3 inflammasome activation, including caspase-1 autocleavage, cytokine release, and pyroptotic cell death in primary macrophages. The inhibitory effects of GC-VLNs on the NLRP3 inflammasome are specific, considering their marginal impact on activation of other inflammasomes. Local administration of GC-VLNs in mice alleviates NLRP3 inflammasome-mediated inflammation in chemical-induced acute liver injury. When administered orally or intravenously, GC-VLNs accumulate in specific tissues and suppress activation of the NLRP3 inflammasome and chronic inflammation in diet-induced obese mice. The phospholipid 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC) in GC-VLNs has been identified to inhibit NLRP3 inflammasome activation. Conclusions: Identification of GC-VLNs and their active component DLPC as potent inflammasome inhibitors provides new therapeutic candidates in the treatment of NLRP3 inflammasome-driven diseases

Critical contributions of protein cargos to the functions of macrophage‑derived extracellular vesicles

Background Macrophages are highly plastic innate immune cells that play key roles in host defense, tissue repair, and homeostasis maintenance. In response to divergent stimuli, macrophages rapidly alter their functions and manifest a wide polarization spectrum with two extremes: M1 or classical activation and M2 or alternative activation. Extracellular vesicles (EVs) secreted from differentially activated macrophages have been shown to have diverse functions, which are primarily attributed to their microRNA cargos. The role of protein cargos in these EVs remains largely unexplored. Therefore, in this study, we focused on the protein cargos in macrophage-derived EVs. Results Naïve murine bone marrow-derived macrophages were treated with lipopolysaccharide or interlukin-4 to induce M1 or M2 macrophages, respectively. The proteins of EVs and their parental macrophages were subjected to quantitative proteomics analyses, followed by bioinformatic analyses. The enriched proteins of M1-EVs were involved in proinflammatory pathways and those of M2-EVs were associated with immunomodulation and tissue remodeling. The signature proteins of EVs shared a limited subset of the proteins of their respective progenitor macrophages, but they covered many of the typical pathways and functions of their parental cells, suggesting their respective M1-like and M2-like phenotypes and functions. Experimental examination validated that protein cargos in M1- or M2-EVs induced M1 or M2 polarization, respectively. More importantly, proteins in M1-EVs promoted viability, proliferation, and activation of T lymphocytes, whereas proteins in M2-EVs potently protected the tight junction structure and barrier integrity of epithelial cells from disruption. Intravenous administration of M2-EVs in colitis mice led to their accumulation in the colon, alleviation of colonic inflammation, promotion of M2 macrophage polarization, and improvement of gut barrier functions. Protein cargos in M2-EVs played a key role in their protective function in colitis. Conclusion This study has yielded a comprehensive unbiased dataset of protein cargos in macrophage-derived EVs, provided a systemic view of their potential functions, and highlighted the important engagement of protein cargos in the pathophysiological functions of these EVs

An immunological electrospun scaffold for tumor cell killing and healthy tissue regeneration

Antibody-based cancer immune therapy has attracted lots of research interest in recent years; however, it is greatly limited by the easy distribution and burst release of antibodies. In addition, after the clearance of the tissue, healthy tissue regeneration is another challenge for cancer treatment. Herein, we have developed a specific immunological tissue engineering scaffold using the agonistic mouse anti-human CD40 antibody (CD40mAb) incorporated into poly(l-lactide) (PLLA) electrospun fibers through the dopamine (PDA) motif (PLLA-PDA-CD40mAb). CD40mAb is successfully incorporated onto the surface of the electrospun fibrous scaffold, which is proved by immunofluorescence staining, and the PLLA-PDA-CD40mAb scaffold has an anti-tumor effect by locally releasing CD40mAb. Therefore, this immunological electrospun scaffold has very good potential to be developed as a powerful tool for localized tumor treatment, and this is the first to be reported in this area

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

Integrated genomic characterization of oesophageal carcinoma

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies