COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Single-cell landscape of immunological responses in patients with COVID-19.

In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between disease severity and the host immune response is not fully understood. Here we performed single-cell RNA sequencing in peripheral blood samples of 5 healthy donors and 13 patients with COVID-19, including moderate, severe and convalescent cases. Through determining the transcriptional profiles of immune cells, coupled with assembled T cell receptor and B cell receptor sequences, we analyzed the functional properties of immune cells. Most cell types in patients with COVID-19 showed a strong interferon-α response and an overall acute inflammatory response. Moreover, intensive expansion of highly cytotoxic effector T cell subsets, such as CD4+ effector-GNLY (granulysin), CD8+ effector-GNLY and NKT CD160, was associated with convalescence in moderate patients. In severe patients, the immune landscape featured a deranged interferon response, profound immune exhaustion with skewed T cell receptor repertoire and broad T cell expansion. These findings illustrate the dynamic nature of immune responses during disease progression.

Sex differences orchestrated by androgens at single-cell resolution.

Sex differences in mammalian complex traits are prevalent and are intimately associated with androgens1-7. However, a molecular and cellular profile of sex differences and their modulation by androgens is still lacking. Here we constructed a high-dimensional single-cell transcriptomic atlas comprising over 2.3 million cells from 17 tissues in Mus musculus and explored the effects of sex and androgens on the molecular programs and cellular populations. In particular, we found that sex-biased immune gene expression and immune cell populations, such as group 2 innate lymphoid cells, were modulated by androgens. Integration with the UK Biobank dataset revealed potential cellular targets and risk gene enrichment in antigen presentation for sex-biased diseases. This study lays the groundwork for understanding the sex differences orchestrated by androgens and provides important evidence for targeting the androgen pathway as a broad therapeutic strategy for sex-biased diseases.

eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health.

eIF3, a multi-subunit complex with numerous functions in canonical translation initiation, is known to interact with 40S and 60S ribosomal proteins and translation elongation factors, but a direct involvement in translation elongation has never been demonstrated. We found that eIF3 deficiency reduced early ribosomal elongation speed between codons 25 and 75 on a set of ∼2,700 mRNAs encoding proteins associated with mitochondrial and membrane functions, resulting in defective synthesis of their encoded proteins. To promote elongation, eIF3 interacts with 80S ribosomes translating the first ∼60 codons and serves to recruit protein quality-control factors, functions required for normal mitochondrial physiology. Accordingly, eIF3e+/- mice accumulate defective mitochondria in skeletal muscle and show a progressive decline in muscle strength. Hence, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for mitochondrial physiology and muscle health.

[Application of high content imaging technique in research on effective components of traditional Chinese medicine: a review].

High content imaging(HCI) technique that combines automatic high throughput with high-resolution cell imaging, is characterized by abundant data information, high imaging sensitivity, easy visualization and standardization, and is commonly used in the cellular(or subcellular) phenotypic analysis. Abundant phenotypic information can be obtained by using HCI in one experiment, including cellular morphology, cellular structure, and signal transduction pathways of related functions, on the basis of the maintenance of the integrity of cellular structures and functions. Multiple studies have shown that a series of dynamic spatio-temporal interactive change processes were induced by the disturbance of cells by specific factors, making cell phenotypes change accordingly, especially for the slight perturbation response of cells. Generally, the detection of one or several endpoint effect indicators is often difficult to accurately and comprehensively reflect the overall efficacy information of traditional Chinese medicine(TCM) because of its unique characteristics of multi-components and multi-targets. The application of HCI is thus helpful to discover the effective components and their action modes in the complex system of TCM. This paper reviewed the application progress in the HCI technique in the screening of active components and their regulation mechanism to provide references for further research.

RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.

BACKGROUND: Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools designed for dissection of the translatome from different aspects. However, as the studies of translation advance quickly, the current toolbox still falls in short, and more specialized tools are in urgent need for deeper and more efficient mining of the important and new features of the translation landscapes. RESULTS: Here, we present RiboMiner, a bioinformatics toolset for mining of multi-dimensional features of the translatome with ribosome profiling data. RiboMiner performs extensive quality assessment of the data and integrates a spectrum of tools for various metagene analyses of the ribosome footprints and for detailed analyses of multiple features related to translation regulation. Visualizations of all the results are available. Many of these analyses have not been provided by previous methods. RiboMiner is highly flexible, as the pipeline could be easily adapted and customized for different scopes and targets of the studies. CONCLUSIONS: Applications of RiboMiner on two published datasets did not only reproduced the main results reported before, but also generated novel insights into the translation regulation processes. Therefore, being complementary to the current tools, RiboMiner could be a valuable resource for dissections of the translation landscapes and the translation regulations by mining the ribosome profiling data more comprehensively and with higher resolution. RiboMiner is freely available at https://github.com/xryanglab/RiboMiner and https://pypi.org/project/RiboMiner .

Comparison of pharmacokinetics of phytoecdysones and triterpenoid saponins of monomer, crude and processed Radix Achyranthis Bidentatae by UHPLC-MS/MS.

1. The aim of this study was to develop a selective, rapid, accurate and sensitive ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for pharmacokinetic (PK) studies of phytoecdysones and triterpenoid saponins after oral administration of five monomers, crude, wine-processed and salt-processed Radix Achyranthis bidentatae (RAB).2. A Thermo Hypersil GOLD C18 column (100 mm × 2.1 mm, 1.9 µm) coupled with a mobile phase of (A) acetonitrile and (B) water (both containing 0.3% acetic acid) was used for sample separation. The mass analysis was performed in a triple quadruple mass spectrometer using selected reaction monitoring (SRM) with negative scan mode.3. The results showed that this method exhibited desirable sensitivity, precision, stability and repeatability. The extraction recoveries of the compounds ranged from 94.2 to 99.8% and the matrix effects ranged from 93.3 to 100.5%. Comparing the Cmax and AUC of five analytes in those groups showed this tendency: salt-processed RAB > wine-processed RAB > crude RAB > monomer group. The results confirmed the feasibility of TCM theory to enhance the efficacy of processed RAB.

De novo annotation and characterization of the translatome with ribosome profiling data.

By capturing and sequencing the RNA fragments protected by translating ribosomes, ribosome profiling provides snapshots of translation at subcodon resolution. The growing needs for comprehensive annotation and characterization of the context-dependent translatomes are calling for an efficient and unbiased method to accurately recover the signal of active translation from the ribosome profiling data. Here we present our new method, RiboCode, for such purpose. Being tested with simulated and real ribosome profiling data, and validated with cell type-specific QTI-seq and mass spectrometry data, RiboCode exhibits superior efficiency, sensitivity, and accuracy for de novo annotation of the translatome, which covers various types of ORFs in the previously annotated coding and non-coding regions. As an example, RiboCode was applied to assemble the context-specific translatomes of yeast under normal and stress conditions. Comparisons among these translatomes revealed stress-activated novel upstream and downstream ORFs, some of which are associated with translational dysregulations of the annotated main ORFs under the stress conditions.

Ursane-type triterpenoids from the roots of Rosa multiflora with their anti-inflammatory activity.

Nine ursane-type triterpenoids including three new ones 2α, 19α-dihydroxyurs-3-O-acetyltormentic acid (1), 1α, 2α, 3α, 20ß-tetrahydroxyurs -13(18)-en-28-oic acid (2), and 2α, 3α, 20ß, 24-tetrahydroxyurs-13(18)-en-28-oic acid (3) were isolated from the roots of Rosa multiflora. Their structures were elucidated by extensive spectroscopic methods, including NMR, MS, and IR spectroscopic analyses data. All the isolates were evaluated for their anti-inflammatory activity in vitro and the results showed that compounds 1-9 displayed moderate inhibitory activity with IC50 values ranging from 24.7 to 86.2 µM compared with the postitive control Amino guanidine (IC50 4.3 µM).[Formula: see text].

A simple liquid chromatography coupled with tandem mass spectrometry approach for the simultaneous quantification of thirteen compounds in rats following oral administration of raw and processed Fructus Xanthii: Application in a comparative pharmacokinetic study.

A simple and sensitive analysis using ultra high performance liquid chromatography with a tandem mass spectrometric system operated in selected reaction monitoring mode was developed for the determination of 11 phenolic acids, atractyloside, and carboxyatractyloside in rat plasma. The two classes of analytes were then separated on a Waters ACQUITY™ UPLC HSS T3 column (50 mm × 2.1 mm, 1.8 µm) using gradient elution with a mobile phase of 0.2% formic acid in water containing 10 mM ammonium acetate and methanol. Detection was accomplished by selected reaction monitoring scanning via an electrospray source operating in negative ionization mode. The calibration curve was linear (R2  = 0.990) over a concentration range of 1.20-3500 ng/mL, while the validated lower limit of quantification was 1.20 ng/mL. The precision varied from 0.84 to 4.62%, and the accuracy varied within ±5%. The method proved robust with sample freezing and thawing and with short- and long-term sample storage. The established method was used for simultaneous quantification and was successfully used for the first time for the pharmacokinetic evaluation of 13 compounds after the intragastric administration of raw and processed Fructus Xanthii in rats. The results indicated that processing affects the absorption and metabolism of Fructus Xanthii extract. Importantly, the results also indicated the importance of processing for the clinical application of traditional Chinese medicine.

Quantitative analysis of different batches of raw, wine-processed, and vinegar-processed Paeoniae Alba Radix using ultra-performance convergence chromatography coupled with photo diode array detection.

Supercritical fluid chromatography is a safe and ecofriendly analytical technique that has not been fully applied to the analysis of traditional Chinese medicine. This is the first study on the separation of six quality markers-paeoniflorin, albiflorin, benzoyl paeoniflorin, oxypaeoniflorin, gallic acid and benzoic acid-from raw, wine-baked and vinegar-baked Paeoniae Alba Radix (PAR) by Supercritical fluid chromatography. Optimum separation was achieved on an HSS C18 SB column (100 × 3.0 mm, 1.8 µm particles) with a gradient elution of high-purity carbon dioxide as mobile phase A and methanol-acetonitrile (70:30, v/v) with 0.10% phosphoric acid as mobile phase B. The flow rate was set at 0.7 mL/min for 15.0 min. The method was validated in terms of the overall intraday and interday precision, with relative standard deviations (RSDs) of 0.87-2.87 and 1.47-3.63%, respectively. The recoveries were 98.10-103.60% with an RSD of 1.00-3.40%. The stability of the RSD values was in the range 1.10-3.78%. The developed approach was successfully applied and provides a valuable reference for the quality assessment of PAR and processed PAR. The results also revealed that the standardization of processing technology is of great significance to the fluctuations in quality before and after the processing of traditional Chinese medicine.

A Biosensor-Based Quantitative Analysis System of Major Active Ingredients in Lonicera japonica Thunb. Using UPLC-QDa and Chemometric Analysis.

In the study, a surface plasmon resonance-based (SPR-based) competitive assay was performed to analyze different compounds' inhibitory activity to TNF-, an important pro-inflammatory cytokine in the pathogenesis of chronic inflammatory diseases. Moreover, the single mass spectrometry (MS) detection method was coupled with an ultra-high-performance liquid chromatography (UPLC) system for the routine quality control (QC) of a traditional Chinese medicine (TCM). The above quality control strategy was evaluated with Lonicera japonica Thunb. Analytes were firstly separated on a Waters ACQUITYTM UPLC HSS T3 column (2.1 × 50 mm; particle size = 1.8 µm) using a 0.1% formic acid gradient elution, then detected by negative ESI mass spectrometry. The limits of quantification (LOQ) for analytes reached 0.005-0.56 µg/mL. The LOD of the QDa detector was lower than that of the PDA detector, indicating its wider detection range. The QDa detector was also more suitable for the analysis of the complex matrix of TCM. The method showed excellent linearity, with regression coefficients higher than 0.9991. The average recoveries of the investigated analytes were in the range of 98.78-105.13%, with an RSD below 3.91%. The inter-day precision range (n = 3 days) was 2.51-4.54%. Compared to other detectors, this strategy could be widely applied in the quantitative analysis of TCM. In addition, the chemically latent data could be revealed using chemometric analysis. Importantly, this study provides an efficient screening method for small-molecule inhibitors targeting the TNF-α pathway.

Simultaneous Determination of Thirteen Q-Markers in Raw and Processed Tussilago farfara L. by UPLC-QQQ-MS/MS Coupled with Chemometrics.

The purpose of this study was to establish a rapid, reliable, and sensitive ultra-performance liquid chromatography with triple-quadrupole tandem mass spectrometry coupled with chemometric method to measure and evaluate the differences between thirteen compounds in raw and processed Tussilago farfara L. from different sources. This assay method was validated, and the results indicated that the calibration curves for the thirteen compounds had good linearity (R² > 0.9990). The limits of detection and limits of quantification of the thirteen compounds ranged from 0.0012 to 0.0095 µg/mL and from 0.0038 to 0.0316 µg/mL, respectively. The relative standard deviations (RSD) of the intra- and inter-day precisions and stability ranged from 1.06 to 2.00%, 0.26 to 1.99%, and 0.75 to 1.97%, respectively. The sample recovery rates of the thirteen compounds with different concentrations were 94.47⁻104.06%. The chemometric results, including principal component analysis, hierarchical clustering analysis, three-dimensional analysis, and box plot analysis, indicated that there are significance differences in raw and processed Tussilago farfara L. The results of this study confirm that the proposed method is the first reported method that has been successfully applied for simultaneous determination and discovery of the difference between thirteen compounds of raw and processed Tussilago farfara L. Thus, this method could be a helpful tool for the detection and confirmation of the quality of traditional Chinese medicines and provide a basis for future pharmacological studies.

HPLC-PDA Combined with Chemometrics for Quantitation of Active Components and Quality Assessment of Raw and Processed Fruits of Xanthium strumarium L.

As a valuable herbal medicine, the fruits of Xanthium strumarium L. (Xanthii Fructus) have been widely used in raw and processed forms to achieve different therapeutic effects in practice. In this study, a comprehensive strategy was proposed for evaluating the active components in 30 batches of raw and processed Xanthii Fructus (RXF and PXF) samples, based on high-performance liquid chromatography coupled with photodiode array detection (HPLC-PDA). Twelve common peaks were detected and eight compounds of caffeoylquinic acids were simultaneously quantified in RXF and PXF. All the analytes were detected with satisfactory linearity (R² > 0.9991) over wide concentration ranges. Simultaneously, the chemically latent information was revealed by hierarchical cluster analysis (HCA) and principal component analysis (PCA). The results suggest that there were significant differences between RXF and PXF from different regions in terms of the content of eight caffeoylquinic acids. Potential chemical markers for XF were found during processing by chemometrics.

UHPLC-MS/MS Quantification Combined with Chemometrics for Comparative Analysis of Different Batches of Raw, Wine-Processed, and Salt-Processed Radix Achyranthis Bidentatae.

An accurate and reliable method using ultra-high performance liquid chromatography combined with triple quadrupole tandem mass spectrometry (UHPLC-MS/MS) was established for simultaneous quantification of five major bioactive analytes in raw, wine-processed, and salt-processed Radix Achyranthis bidentatae (RAB). The results showed that this method exhibited desirable sensitivity, precision, stability, and repeatability. The overall intra-day and inter-day variations (RSD) were in the range of 1.57-2.46 and 1.51-3.00%, respectively. The overall recoveries were 98.58-101.48% with a relative standard deviation (RSD) of 0.01-1.86%. In addition, the developed approach was applied to 21 batches of raw, wine-processed, and salt-processed samples of RAB. Hierarchical clustering analysis (HCA), principal component analysis (PCA), heat map, and boxplot analysis were performed to evaluate the quality of raw, wine-processed, and salt-processed RAB collected from different regions. The chemometrics combined with the quantitative analysis based on UHPLC-MS/MS results indicated that the content of five analytes increased significantly in processed RAB compared to raw RAB.

[Study on lignans from Xanthii Fructus].

This project is to investigate lignans from the dried fruits of Xanthium sibiricum (Xanthii Fructus). The chemical constituents were extract by 70% ethanol and isolated by silica gel, ODS, Sephadex LH-20, MCI column chromatography. Based on comparison of their spectral data with those reported in literature, they were elucidated as (-)-pinoresinol (1), balanophonin A (2), diospyrosin (3), dehydrodiconiferyl alcohol (4), 2-(4-hydroxy-3-methoxyphenyl)-3-(2-hydroxy-5-methoxyphenyl)-3-oxo-1-propanol (5), (-)-simulanol (6), (-)-7R,8S-dehydrodiconiferyl alcohol (7), chushizisin E (8), dihydrodehydrodiconiferyl alcohol (9), 7R,8S-dihydrodehydrodiconiferyl alcohol 4-O-ß-D-glucopyranoside (10), erythro-1,2-bis(4-hydroxy-3-methoxyphenyl)-1,3-propanediol (11), leptolepisol D (12), 8-O-4' neolignan 4-O-ß-glucopyranoside (13), (-)-1-O-ß-D-glucopyranosyl-2-{2-methoxy-4-[1-(E)-propen-3-ol]phenoxyl}-propane-3-ol(14), 1-(4-hydroxy-3-methoxy)-phenyl-2-[4-(1,2,3-trihydroxypropyl)-2-methoxy]-phenoxy-1,3-propandiol (15), threo-dihydroxy dehydrodiconiferyl alcohol (16), (-)-(2R)-1-O-ß-D-glucopyranosyl-2-{2-methoxy-4-[(E)-formylviny1]phenoxyl} propane-3-ol (17). Compound 2-17 were isolated from the genus Xanthium for the first time. Compound 1 were isolated form Xanthii Fructus for the first time.

Magnetic resonance imaging evaluation of residual tumors in breast cancer after neoadjuvant chemotherapy: surgical implications.

BACKGROUND: Magnetic resonance imaging (MRI) can be used to guide breast cancer surgery with breast conservation for large tumors with a substantially reduced size after neoadjuvant chemotherapy (NAC). PURPOSE: To evaluate the value of dynamic contrast-enhanced MRI (DCE-MRI) for measuring residual tumor size and enhancement patterns following preoperative NAC. MATERIAL AND METHODS: Eighty-nine patients with breast cancer underwent breast DCE-MRI; 38 patients (39 lesions) were treated with NAC and examined for residual disease following therapy. Two patients were excluded because surgery had been performed >2 weeks after the final MR examination. Thus, we correlated the DCE-MRI results of 36 patients (37 lesions) with postoperative histopathological findings. Residual disease was confirmed by more enhancement compared to normal glandular tissue at the initial tumor site. Residual tumor size on DCE-MRI was compared with postoperative pathology findings. Tumor enhancement patterns on DCE-MRI were analyzed and correlated with pathological classification. RESULTS: MRI revealed 34 cases of residual tumors, with two false positives and one false negative. Pathological and MR measurements were correlated (r = 0.793). The correlation of mass enhancement size (r = 0.87, n = 14) with pathology and DCE-MRI was higher than for non-mass-like enhancement (NME) (r = 0.735, n = 23). The distribution of pathologic classification was significantly different between different MRI enhancement patterns (P = 0.006). Mass enhancement had higher cellularity than NME. CONCLUSION: MRI is useful for evaluating residual carcinoma following NAC. Mass enhancement with higher cellularity after NAC can be evaluated more accurately, which is suitable for evaluating lumpectomy. However, other approaches are required for NME, which has lower cellularity.

Distinct roles of TREM2 in central nervous system cancers and peripheral cancers.

Glioblastomas (GBM) are incurable central nervous system (CNS) cancers characterized by substantial myeloid cell infiltration. Whether myeloid cell-directed therapeutic targets identified in peripheral non-CNS cancers are applicable to GBM requires further study. Here, we identify that the critical immunosuppressive target in peripheral cancers, triggering receptor expressed on myeloid cells-2 (TREM2), is immunoprotective in GBM. Genetic or pharmacological TREM2 deficiency promotes GBM progression in vivo. Single-cell and spatial sequencing reveals downregulated TREM2 in GBM-infiltrated myeloid cells. TREM2 negatively correlates with immunosuppressive myeloid and T cell exhaustion signatures in GBM. We further demonstrate that during GBM progression, CNS-enriched sphingolipids bind TREM2 on myeloid cells and elicit antitumor responses. Clinically, high TREM2 expression in myeloid cells correlates with better survival in GBM. Adeno-associated virus-mediated TREM2 overexpression impedes GBM progression and synergizes with anti-PD-1 therapy. Our results reveal distinct functions of TREM2 in CNS cancers and support organ-specific myeloid cell remodeling in cancer immunotherapy.