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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., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Sex differences in mammalian complex traits are prevalent and are intimately associated with androgens 1-7 . 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., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Metabolic fitness of T cells is essential for their vitality, which is largely dependent on the behavior of the mitochondria. The nature of mitochondrial behavior in tumor-infiltrating T cells remains poorly understood. In this study, we show that mitofusin-2 (MFN2) expression is positively correlated with the prognosis of multiple cancers. Genetic ablation of Mfn2 in CD8 + T cells dampens mitochondrial metabolism and function and promotes tumor progression. In tumor-infiltrating CD8 + T cells, MFN2 enhances mitochondria-endoplasmic reticulum (ER) contact by interacting with ER-embedded Ca 2+ -ATPase SERCA2, facilitating the mitochondrial Ca 2+ influx required for efficient mitochondrial metabolism. MFN2 stimulates the ER Ca 2+ retrieval activity of SERCA2, thereby preventing excessive mitochondrial Ca 2+ accumulation and apoptosis. Elevating mitochondria-ER contact by increasing MFN2 in CD8 + T cells improves the efficacy of cancer immunotherapy. Thus, we reveal a tethering-and-buffering mechanism of organelle cross-talk that regulates the metabolic fitness of tumor-infiltrating CD8 + T cells and highlights the therapeutic potential of enhancing MFN2 expression to optimize T cell function.

The chemical complexity of traditional Chinese medicines (TCMs) makes the active and functional annotation of natural compounds challenging. Herein, we developed the TCMs-Compounds Functional Annotation platform (TCMs-CFA) for large-scale predicting active compounds with potential mechanisms from TCM complex system, without isolating and activity testing every single compound one by one. The platform was established based on the integration of TCMs knowledge base, chemome profiling, and high-content imaging. It mainly included: (1) selection of herbal drugs of target based on TCMs knowledge base; (2) chemome profiling of TCMs extract library by LC‒MS; (3) cytological profiling of TCMs extract library by high-content cell-based imaging; (4) active compounds discovery by combining each mass signal and multi-parametric cell phenotypes; (5) construction of functional annotation map for predicting the potential mechanisms of lead compounds. In this stud TCMs with myocardial protection were applied as a case study, and validated for the feasibility and utility of the platform. Seven frequently used herbal drugs ( Ginseng , etc.) were screened from 100,000 TCMs formulas for myocardial protection and subsequently prepared as a library of 700 extracts. By using TCMs-CFA platform, 81 lead compounds, including 10 novel bioactive ones, were quickly identified by correlating 8089 mass signals with 170,100 cytological parameters from an extract library. The TCMs-CFA platform described a new evidence-led tool for the rapid discovery process by data mining strategies, which is valuable for novel lead compounds from TCMs. All computations are done through Python and are publicly available on GitHub., Competing Interests: The authors declare no conflicts of interest., (© 2023 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.)

This study applied territorial spatial planning control to a land use multi-scenario simulation in Changde, China, and measured the landscape ecological risk response. It embedded five planning control schemes, respectively, involving inertial development, urban expansion size quantity control, ecological spatial structure control, land use zoning control, and comprehensive control. Findings show that: (1) Woodland and arable land in Changde occupy 31.10% and 43.35% of land use, respectively, and constitute the main functional space of the research area. The scale of construction land in Changde has enlarged continuously, with ecological space represented by woodland and water constantly squeezed and occupied. (2) Comprehensive control has the most remarkable restraining effect on the disordered spread of construction land, while ecological space structure control is the most effective way to control ecological land shrinkage. (3) The overall landscape ecological risk index expanded over 2009-2018, presenting an S-type time evolution curve of "sharp increase-mitigation". Landscape ecological risk presents a single-core, double-layer circle structure with the north and east regions as the core, attenuating to the periphery. (4) Landscape ecological risk under land use zoning control increased significantly more than in other scenarios. Comprehensive control best prevented landscape ecological risk and restrained the disorderly expansion of construction land., Competing Interests: Yong Zhang employed by Hunan Sidayuan Planning Consulting Research Co., Ltd., on 30 May 2020 in the library, and he declares the following on the conflict of interest: I promise to avoid conflicts of interest (even superficial conflicts) with the company, its shareholders, and its customers. I endeavor to ensure that my personal conduct is in accordance with the following guidelines and to report appropriately when there is a potential for actual or potential conflict. These conflicts of interest may be caused by my immediate family members, other members of my family, or stakeholders. Therefore, the prohibited sexual behaviors involved in this commitment also involve my immediate family members, other members of my family, or stakeholders. I promise that I will write to the president or vice president of the company about the conflicts of interest caused or possible to be caused by my immediate family members, other members of my family, or stakeholders Presentation. The remaining authors declare no conflict of interest.

Characterization of the dynamic change in the immunological landscape during malignant transformation from precancerous lesions to cancerous lesions in squamous cell carcinoma (SCC) is critical for the application of immunotherapy. Here, we performed single-cell RNA-Seq (scRNA-Seq) of 131,702 cells from 13 cancerous tissues of oral squamous cell carcinoma (OSCC), 3 samples of precancerous oral leukoplakia, and 8 adjacent normal samples. We found that tumor-infiltrating CD4+ and CD8+ T cells were functionally inhibited by immunosuppressive ligands expressed on various types of myeloid cells or neutrophils in the process of oral carcinogenesis. Notably, we identified a subset of myofibroblasts that exclusively expressed tryptophan 2,3-dioxygenase (TDO2). These TDO2+ myofibroblasts were located distally from tumor nests, and both CD4+ and CD8+ T cells were enriched around them. Functional experiments revealed that TDO2+ myofibroblasts were more likely to possess the ability for chemotaxis toward T cells but induced the transformation of CD4+ T cells into Tregs and caused CD8+ T cell dysfunction. We further showed that use of the TDO2 inhibitor LM10 attenuated the inhibitory states of T cells, restored the T cell antitumor response, and prevented the progression of OSCC malignant transformation in murine models. Our study reveals a multistep transcriptomic landscape of OSCC and demonstrates that TDO2+ myofibroblasts are potential targets for immunotherapy.

To obtain a comprehensive scenario of T cell profiles and synergistic immune responses, we performed single-cell RNA sequencing (scRNA-seq) on the peripheral T cells of 14 individuals with chronic human immunodeficiency virus 1 (HIV-1) infection, including nine treatment-naive (TP) and eight antiretroviral therapy (ART) participants (of whom three were paired with TP cases), and compared the results with four healthy donors (HD). Through analyzing the transcriptional profiles of CD4 + and CD8 + T cells, coupled with assembled T cell receptor sequences, we observed the significant loss of naive T cells, prolonged inflammation, and increased response to interferon-α in TP individuals, which could be partially restored by ART. Interestingly, we revealed that CD4 + and CD8 + Effector-GNLY clusters were expanded in TP cases, and persistently increased in ART individuals where they were typically correlated with poor immune restoration. This transcriptional dataset enables a deeper understanding of the pathogenesis of HIV-1 infection and is also a rich resource for developing novel immune targeted therapeutic strategies., (© 2022. The Author(s).)

Lung cancer is the leading cause of cancer mortality, and early detection is key to improving survival. However, there are no reliable blood-based tests currently available for early-stage lung cancer diagnosis. Here, we performed single-cell RNA sequencing of different early-stage lung cancers and found that lipid metabolism was broadly dysregulated in different cell types, with glycerophospholipid metabolism as the most altered lipid metabolism-related pathway. Untargeted lipidomics was carried out in an exploratory cohort of 311 participants. Through support vector machine algorithm-based and mass spectrum-based feature selection, we identified nine lipids (lysophosphatidylcholines 16:0, 18:0, and 20:4; phosphatidylcholines 16:0-18:1, 16:0-18:2, 18:0-18:1, 18:0-18:2, and 16:0-22:6; and triglycerides 16:0-18:1-18:1) as the features most important for early-stage cancer detection. Using these nine features, we developed a liquid chromatography-mass spectrometry (MS)-based targeted assay using multiple reaction monitoring. This target assay achieved 100.00% specificity on an independent validation cohort. In a hospital-based lung cancer screening cohort of 1036 participants examined by low-dose computed tomography and a prospective clinical cohort containing 109 participants, the assay reached more than 90.00% sensitivity and 92.00% specificity. Accordingly, matrix-assisted laser desorption/ionization MS imaging confirmed that the selected lipids were differentially expressed in early-stage lung cancer tissues in situ. This method, designated as Lung Cancer Artificial Intelligence Detector, may be useful for early detection of lung cancer or large-scale screening of high-risk populations for cancer prevention.

Background: Neurotropic virus infection can cause serious damage to the central nervous system (CNS) in both humans and animals. The complexity of the CNS poses unique challenges to investigate the infection of these viruses in the brain using traditional techniques., Methods: In this study, we explore the use of fluorescence micro-optical sectioning tomography (fMOST) and single-cell RNA sequencing (scRNA-seq) to map the spatial and cellular distribution of a representative neurotropic virus, rabies virus (RABV), in the whole brain. Mice were inoculated with a lethal dose of a recombinant RABV encoding enhanced green fluorescent protein (EGFP) under different infection routes, and a three-dimensional (3D) view of RABV distribution in the whole mouse brain was obtained using fMOST. Meanwhile, we pinpointed the cellular distribution of RABV by utilizing scRNA-seq., Results: Our fMOST data provided the 3D view of a neurotropic virus in the whole mouse brain, which indicated that the spatial distribution of RABV in the brain was influenced by the infection route. Interestingly, we provided evidence that RABV could infect multiple nuclei related to fear independent of different infection routes. More surprisingly, our scRNA-seq data revealed that besides neurons RABV could infect macrophages and the infiltrating macrophages played at least three different antiviral roles during RABV infection., Conclusion: This study draws a comprehensively spatial and cellular map of typical neurotropic virus infection in the mouse brain, providing a novel and insightful strategy to investigate the pathogenesis of RABV and other neurotropic viruses., (© 2022 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)

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., Competing Interests: Declaration of interests Zemin Zhang is a founder of Analytical Bioscience and an advisor for InnoCare. All financial interests are unrelated to this study. The remining authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Cells mitigate ER stress through the unfolded protein response (UPR). Here, we report formation of ER whorls as an effector mechanism of the ER stress response. We found that strong ER stress induces formation of ER whorls, which contain ER-resident proteins such as the Sec61 complex and PKR-like ER kinase (PERK). ER whorl formation is dependent on PERK kinase activity and is mediated by COPII machinery, which facilitates ER membrane budding to form tubular-vesicular ER whorl precursors. ER whorl precursors then go through Sec22b-mediated fusion to form ER whorls. We further show that ER whorls contribute to ER stress-induced translational inhibition by possibly modulating PERK activity and by sequestering translocons in a ribosome-free environment. We propose that formation of ER whorls reflects a new type of ER stress response that controls inhibition of protein translation.

Lung adenocarcinomas (LUAD) that radiologically display as subsolid nodules (SSNs) exhibit more indolent biological behavior than solid LUAD. The transcriptomic features and tumor microenvironment (TME) of SSN remain poorly understood. Here, we performed single-cell RNA sequencing analyses of 16 SSN samples, 6 adjacent normal lung tissues (nLung), and 9 primary LUAD with lymph node metastasis (mLUAD). Approximately 0.6 billion unique transcripts were obtained from 118,293 cells. We found that cytotoxic natural killer/T cells were dominant in the TME of SSN, and malignant cells in SSN undergo a strong metabolic reprogram and immune stress. In SSN, the subtype composition of endothelial cells was similar to that in mLUAD, while the subtype distribution of fibroblasts was more like that in nLung. Our study provides single-cell transcriptomic profiling of SSN and their TME. This resource provides deeper insight into the indolent nature of SSN and will be helpful in advancing lung cancer immunotherapy., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

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.

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., Competing Interests: Declaration of Interests D.A.W. is a part-time resident in medical genetics at MGZ Medical Genetics Center, Munich, Germany. The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

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 .

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 C max 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.

Two new monoterpene glucosides: xanmonoter A (1) and xanmonoter B ( 2 ) were isolated from Xanthium strumarium . Their structures were elucidated on the basis of 1D and 2D NMR, MS and CD analysis. Compounds 1 and 2 were tested for their anti-inflammatory activity with IC 50 values of 17.4, 22.1 μM, respectively.

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 (R 2  = 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., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step., (© The Author(s) (2019). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS.)

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 C 18 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., (© 2019 John Wiley & Sons, Ltd.)

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., Competing Interests: The authors declare no conflicts of interest.

Background: As a widely used toxic traditional herbal medicine, the quality of the Fructus Xanthii must be well controlled to ensure the clinical therapeutic efficacy and safety., Aims: A rapid, and sensitive using ultra-high performance liquid chromatography to triple quadrupole tandem mass spectrometry (UPLC-MS/MS) in selected reaction monitoring (SRM) mode was developed and validated for simultaneous quantitation of determination active and toxic ingredients form processed by stir-frying and raw materials of Fructus Xanthii., Methods: Chromatographic separation of all targeted compound was performed on Waters ACQUITY UPLC HSS T3 column (50 mm × 2.1 mm, 1.8 μm). Moreover, the method was successfully applied in thirty-six samples of Fructus Xanthii collected from different sources in China. The processing method was optimized through Box-Behnken statistical design and response surface methodology., Results: In this work, chemometrics was able to successfully discriminate and classify among samples. The optimal incubation conditions were as follows: under heating in a pot at 295 °C, medicine at 120 °C for 11.0 min with flipping frequently., Conclusions: Therefore, the established UPLC-QQQ-MS method in combination with chemometric analysis provides a rapid, flexible and reliable method for quality assessment of Fructus Xanthii. Importantly, the optimized experimental value of the processing process provides the basis for future research., (Copyright © 2018. Published by Elsevier GmbH.)

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.

The ripe fruit of Xanthium strumarium L. (Xanthii Fructus) cannot be widely used as a Chinese herbal medicine (CHM) owing to its hepatotoxicity. However, Xanthii Fructus (XF) can be used effectively and safely after correct processing based on traditional experience, although a high hepatotoxicity risk remains owing to improper usage. Therefore, the processing methods used must be clarified to ensure safety. The adenosine-5'-triphosphate (ATP) level in tissues is an important indicator reflecting the functional status of liver cells. Therefore, this study aims to evaluate the hepatotoxicity of XF using UPLC-MS/MS. The hepatotoxicity of raw XF (RXF) and XF processed by intermediary energy metabolites (PXF) is compared. The method is evaluated for its analytical performance and successfully applied to the quantification of ATP, adenosine-5'-diphosphate (ADP), adenosine-5'-monophosphate (AMP), atractyloside, and carboxyatractyloside in mouse liver. The hepatotoxicity results also indicate that the toxicity of XF is decreased after processing, perhaps due to the decrease in atractyloside and carboxyatractyloside contents. Importantly, the experimental evidence provides a rationale for the reduction in toxicity. These data show that mouse livers are damaged between the days 20 and 30 of RXF oral administration, and that the ATP level is decreased. Importantly, no significant difference is observed between the PXF treatment group and control group, while the RXF treatment group is significantly different. Therefore, processing can reduce the toxicity of XF., Competing Interests: There are no conflicts of interest to declare., (This journal is © The Royal Society of Chemistry.)

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.

Phenolic acids are important active components of certain Traditional Chinese Medicines (TCM) and have a wide range of biological effects. Separation and purification of phenolic acids remains challenging due to difficulties with quality control using existing chromatographic methods The purpose of this study was to compare the effects of different chromatographic columns and conditions for the separation of phenolic acids. The BEH column was determined to be optimal, providing efficient separation in the shortest time (17.00 min) using gradient elution with carbon dioxide as the mobile phase, methanol/acetonitrile (70:30, v/v) with 1% TFA as the modifier, and a flow rate of 0.8 mL/min. Good peak shapes were obtained, and the peak asymmetry values were close to 1.00 for all phenolic acids. The resolution was more than 2.83 for all separated peaks. The developed method was subsequently applied to the determination of phenolic acids in Xanthii Fructus. These results are beneficial for quality control and standardization of herbal drugs using UPC 2 , providing an efficient, rapid and environmentally friendly scientific basis for future analysis of phenolic acids., (Copyright © 2018. Published by Elsevier B.V.)

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., Competing Interests: The authors declare no conflict of interest.

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., Competing Interests: The authors have no conflicts of interest to declare.

Spermatogenesis is a differentiation process during which diploid spermatogonial stem cells (SSCs) produce haploid spermatozoa. This highly specialized process is precisely controlled at the transcriptional, posttranscriptional, and translational levels. Here we report that N 6 -methyladenosine (m 6 A), an epitranscriptomic mark regulating gene expression, plays essential roles during spermatogenesis. We present comprehensive m 6 A mRNA methylomes of mouse spermatogenic cells from five developmental stages: undifferentiated spermatogonia, type A 1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids. Germ cell-specific inactivation of the m 6 A RNA methyltransferase Mettl3 or Mettl14 with Vasa-Cre causes loss of m 6 A and depletion of SSCs. m 6 A depletion dysregulates translation of transcripts that are required for SSC proliferation/differentiation. Combined deletion of Mettl3 and Mettl14 in advanced germ cells with Stra8-GFPCre disrupts spermiogenesis, whereas mice with single deletion of either Mettl3 or Mettl14 in advanced germ cells show normal spermatogenesis. The spermatids from double-mutant mice exhibit impaired translation of haploid-specific genes that are essential for spermiogenesis. This study highlights crucial roles of mRNA m 6 A modification in germline development, potentially ensuring coordinated translation at different stages of spermatogenesis.

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., (© The Foundation Acta Radiologica 2015.)

Acquiring comprehensive knowledge of protein in various subcellular localizations is one of the fundamental goals in cell biology and proteomics. Although recent large-scale experimental and proteomics studies of S. cerevisiae protein subcellular localizations are archived in various databases, only a few studies use a systems biology approach to characterize S. cerevisiae proteins at a subcellular localization level. Based on the topological properties and biological properties of S. cerevisiae proteins, we have compared, contrasted and analyzed the statistical properties across eight different subcellular localizations. Significant differences are found in all topological properties and biological properties among eight protein categories. Network topology analysis indicates that the nuclear proteins differ from the other seven protein categories, and tend to have the most important topological properties and play an important role in the network, including the highest degree, core number, and betweenness centrality. In the light of the above, we hope these findings presented in this study may provide important help for protein subcellular localization prediction in S. cerevisiae and provide many new insights for understanding the proteins directly from subcellular localizations.