High-throughput transcriptional profiling of perturbations by Panax ginseng saponins and Panax notoginseng saponins using TCM-seq / 药物分析学报

Panax ginseng(PG)and Panax notoginseng(PN)are highly valuable Chinese medicines(CM).Although both CMs have similar active constituents,their clinical applications are clearly different.Over the past decade,RNA sequencing(RNA-seq)analysis has been employed to investigate the molecular mechanisms of extracts or monomers.However,owing to the limited number of samples in standard RNA-seq,few studies have systematically compared the effects of PG and PN spanning multiple conditions at the transcriptomic level.Here,we developed an approach that simultaneously profiles transcriptome changes for multiplexed samples using RNA-seq(TCM-seq),a high-throughput,low-cost workflow to molecularly evaluate CM perturbations.A species-mixing experiment was conducted to illustrate the accuracy of sample multiplexing in TCM-seq.Transcriptomes from repeated samples were used to verify the robustness of TCM-seq.We then focused on the primary active components,Panax notoginseng sa-ponins(PNS)and Panax ginseng saponins(PGS)extracted from PN and PG,respectively.We also char-acterized the transcriptome changes of 10 cell lines,treated with four different doses of PNS and PGS,using TCM-seq to compare the differences in their perturbing effects on genes,functional pathways,gene modules,and molecular networks.The results of transcriptional data analysis showed that the tran-scriptional patterns of various cell lines were significantly distinct.PGS exhibited a stronger regulatory effect on genes involved in cardiovascular disease,whereas PNS resulted in a greater coagulation effect on vascular endothelial cells.This study proposes a paradigm to comprehensively explore the differences in mechanisms of action between CMs based on transcriptome readouts.

Investigation of endothelial cell pathological characteristics in murine choroidal neovascularization model based on single-cell RNA sequencing / 中华实验眼科杂志

Objective:To investigate the molecular expression and pathological features of endothelial cell (EC) in a murine model of choroidal neovascularization (CNV) based on single-cell RNA sequencing (scRNA-seq).Methods:Six C57BL/6 mice aged 6-8 weeks were randomly divided into two groups, with 3 mice in each group.Bilateral eyeballs were enucleated.The choroidal tissues from the two groups were isolated by shearing the complex and scraping the choroid, respectively.Single-cell suspension was prepared by continuous digestion with trypsin/type Ⅰ collagenase at 37 ℃, and the cell viability and EC ratio were detected by flow cytometry to determine the preparation method of single-cell suspension.Another 6 mice were randomly assigned into the control group and the CNV group, with 3 mice in each group.The CNV model was induced by laser photocoagulation and single-cell suspensions were prepared 7 days after modeling.Gene expression library construction was performed using the Chromi-um (10x Genomics) instrument.High throughput sequencing was performed using the Illumina Novaseq6000 to obtain the expression matrix.The EC subpopulations were classified according to previous researches and the Cellmarker database.Pseudo-time analysis was performed in EC, revealing the gene expression matrix of different states.CNV-EC were further selected with preliminary analysis of the expression characteristics.Another 6 mice were selected to establish the CNV model and eyeball frozen sections were prepared 7 days after modeling.Expression and distribution as well as the area percentage of EC marker Pecam1, mitochondrial outer membrane proteins Tomm20 and mt-Co1, and capillary markers Kdr and Plvap were observed by immunofluorescence staining, and the vascular diameter was calculated.The use and care of animals followed the ARVO statement.This study protocol was approved by the Experimental Animal Welfare and Ethics Committee of Air Force Military Medical University (No.20200181).Results:The cell viability of the single-cell suspension prepared from choroidal-scleral fragments and choroidal scrapings was 99.4% and 99.1%, respectively, both of which met the sequencing requirements.The percentage of EC detected by flow cytometry was approximately 1.58%.The scRNA-seq result revealed that both the normal control and CNV groups contained 13 choroidal cell clusters.Compared with the normal control group, the proportions of rod/cone photoreceptor cells, EC and hematopoietic cells all increased, while the retinal pigment epithelium (RPE) and Schwan cells reduced in the CNV group.Among all clusters, EC constituted 18.4%.The pseudo-time analysis demonstrated that EC could be further divided into 4 states.The percentage of state 2 EC was 29.1% in the CNV group, which was significantly higher than 9.5% in the normal control group.Differentially expressed gene analysis showed that the expression of mitochondrion-related genes, including mt-Nd4 and mt-Atp6, were upregulated in state 2 EC, while capillary-related genes, including Kdr and Esm1, were downregulated.Immunofluorescent staining revealed that the area of Tomm20 and mt-Co1 in Pecam1-positive EC in the CNV area was (19.50±4.68)% and (4.64±2.82)%, respectively, which were both higher than (3.00±2.09)% and (0.18±0.34)% in normal area ( t=7.88, 3.84; both at P<0.01). The area of Kdr and Plvap in Pecam1-positive EC in the CNV area was (1.50±0.29)% and (0.79±0.97)%, respectively, which were both lower than (31.30±5.44)% and (10.43±2.28)% in the normal area ( t=13.40, 9.48; both at P<0.01). The vascular diameter in the CNV area was (5.52±1.85)μm, which was larger than (4.21±1.84)μm in the normal area ( t=9.57, P<0.001). Conclusions:When CNV occurs, the proportion of EC in choroid increases, and CNV-EC shows pathologic features of mitochondrial metabolic activation and loss of capillary properties, suggesting the mitochondrial activation of EC may play a role in the formation of CNV.

Evaluation of peripheral blood T-lymphocyte subpopulations features in patients with hepatitis B virus-related acute-on-chronic liver failure based on single-cell sequencing technology / 中华肝脏病杂志

Objective: T lymphocyte exhaustion is an important component of immune dysfunction. Therefore, exploring peripheral blood-exhausted T lymphocyte features in patients with hepatitis B virus-related acute-on-chronic liver failure may provide potential therapeutic target molecules for ACLF immune dysfunction. Methods: Six cases with HBV-ACLF and three healthy controls were selected for T-cell heterogeneity detection using the single-cell RNA sequencing method. In addition, exhausted T lymphocyte subpopulations were screened to analyze their gene expression features, and their developmental trajectories quasi-timing. An independent sample t-test was used to compare the samples between the two groups. Results: Peripheral blood T lymphocytes in HBV-ACLF patients had different differentiation trajectories with different features distinct into eight subpopulations. Among them, the CD4(+)TIGIT(+) subsets (P = 0.007) and CD8(+)LAG3(+) (P = 0.010) subsets with highly exhausted genes were significantly higher than those in healthy controls. Quasi-time analysis showed that CD4(+)TIGIT(+) and CD8(+)LAG3(+) subsets appeared in the late stage of T lymphocyte differentiation, suggesting the transition of T lymphocyte from naïve-effector-exhausted during ACLF pathogenesis. Conclusion: There is heterogeneity in peripheral blood T lymphocyte differentiation in patients with HBV-ACLF, and the number of exhausted T cells featured by CD4(+)TIGIT(+)T cell and CD8(+)LAG3(+) T cell subsets increases significantly, suggesting that T lymphocyte immune exhaustion is involved in the immune dysfunction of HBV-ACLF, thereby identifying potential effective target molecules for improving ACLF patients' immune function.

Single-cell profiling reveals a potent role of quercetin in promoting hair regeneration

Hair loss affects millions of people at some time in their life, and safe and efficient treatments for hair loss are a significant unmet medical need. We report that topical delivery of quercetin (Que) stimulates resting hair follicles to grow with rapid follicular keratinocyte proliferation and replenishes perifollicular microvasculature in mice. We construct dynamic single-cell transcriptome landscape over the course of hair regrowth and find that Que treatment stimulates the differentiation trajectory in the hair follicles and induces an angiogenic signature in dermal endothelial cells by activating HIF-1α in endothelial cells. Skin administration of a HIF-1α agonist partially recapitulates the pro-angiogenesis and hair-growing effects of Que. Together, these findings provide a molecular understanding for the efficacy of Que in hair regrowth, which underscores the translational potential of targeting the hair follicle niche as a strategy for regenerative medicine, and suggest a route of pharmacological intervention that may promote hair regrowth.

Single-nucleus transcriptomics reveals a gatekeeper role for FOXP1 in primate cardiac aging

Aging poses a major risk factor for cardiovascular diseases, the leading cause of death in the aged population. However, the cell type-specific changes underlying cardiac aging are far from being clear. Here, we performed single-nucleus RNA-sequencing analysis of left ventricles from young and aged cynomolgus monkeys to define cell composition changes and transcriptomic alterations across different cell types associated with age. We found that aged cardiomyocytes underwent a dramatic loss in cell numbers and profound fluctuations in transcriptional profiles. Via transcription regulatory network analysis, we identified FOXP1, a core transcription factor in organ development, as a key downregulated factor in aged cardiomyocytes, concomitant with the dysregulation of FOXP1 target genes associated with heart function and cardiac diseases. Consistently, the deficiency of FOXP1 led to hypertrophic and senescent phenotypes in human embryonic stem cell-derived cardiomyocytes. Altogether, our findings depict the cellular and molecular landscape of ventricular aging at the single-cell resolution, and identify drivers for primate cardiac aging and potential targets for intervention against cardiac aging and associated diseases.

Single-nucleus profiling unveils a geroprotective role of the FOXO3 in primate skeletal muscle aging

Age-dependent loss of skeletal muscle mass and function is a feature of sarcopenia, and increases the risk of many aging-related metabolic diseases. Here, we report phenotypic and single-nucleus transcriptomic analyses of non-human primate skeletal muscle aging. A higher transcriptional fluctuation was observed in myonuclei relative to other interstitial cell types, indicating a higher susceptibility of skeletal muscle fiber to aging. We found a downregulation of FOXO3 in aged primate skeletal muscle, and identified FOXO3 as a hub transcription factor maintaining skeletal muscle homeostasis. Through the establishment of a complementary experimental pipeline based on a human pluripotent stem cell-derived myotube model, we revealed that silence of FOXO3 accelerates human myotube senescence, whereas genetic activation of endogenous FOXO3 alleviates human myotube aging. Altogether, based on a combination of monkey skeletal muscle and human myotube aging research models, we unraveled the pivotal role of the FOXO3 in safeguarding primate skeletal muscle from aging, providing a comprehensive resource for the development of clinical diagnosis and targeted therapeutic interventions against human skeletal muscle aging and the onset of sarcopenia along with aging-related disorders.

Acute Developmental Toxicity of Panax notoginseng in Zebrafish Larvae / 中国结合医学杂志

OBJECTIVE@#To evaluate toxicity of raw extract of Panax notoginseng (rPN) and decocted extract of PN (dPN) by a toxicological assay using zebrafish larvae, and explore the mechanism by RNA sequencing assay.@*METHODS@#Zebrafish larvae was used to evaluate acute toxicity of PN in two forms: rPN and dPN. Three doses (0.5, 1.5, and 5.0 µ g/mL) of dPN were used to treat zebrafishes for evaluating the developmental toxicity. Behavior abnormalities, body weight, body length and number of vertebral roots were used as specific phenotypic endpoints. RNA sequencing (RNA-seq) assay was applied to clarify the mechanism of acute toxicity, followed by real time PCR (qPCR) for verification. High performance liquid chromatography analysis was performed to determine the chemoprofile of this herb.@*RESULTS@#The acute toxicity result showed that rPN exerted higher acute toxicity than dPN in inducing death of larval zebrafishes (P<0.01). After daily oral intake for 21 days, dPN at doses of 0.5, 1.5 and 5.0 µ g/mL decreased the body weight, body length, and vertebral number of larval zebrafishes, indicating developmental toxicity of dPN. No other adverse outcome was observed during the experimental period. RNA-seq data revealed 38 genes differentially expressed in dPN-treated zebrafishes, of which carboxypeptidase A1 (cpa1) and opioid growth factor receptor-like 2 (ogfrl2) were identified as functional genes in regulating body development of zebrafishes. qPCR data showed that dPN significantly down-regulated the mRNA expressions of cpa1 and ogfrl2 (both P<0.01), verifying cpa1 and ogfrl2 as target genes for dPN.@*CONCLUSION@#This report uncovers the developmental toxicity of dPN, suggesting potential risk of its clinical application in children.

Preliminary Results of Single-cell Transcriptome Sequencing in Renal Arterial Lesions of Takayasu Arteritis / 中国医学科学院学报

Objective To explore the preliminary application of single-cell RNA sequencing (scRNA-seq) in the renal arterial lesions in Takayasu arteritis (TA) patients. Methods This study included 2 TA patients with renal artery stenosis treated by bypass surgery in the Department of Vascular Surgery,Beijing Hospital.The obtained 2 renal artery samples were digested with two different protocols (GEXSCOPE kit and self-made digestion liquid) before scRNA-seq and bioinformatics analysis. Results A total of 2920 cells were obtained for further analysis.After unbiased cluster analysis,2 endothelial cell subsets,2 smooth muscle cell subsets,1 fibroblast subset,2 mononuclear macrophage subsets,1 T cell subset,and 1 undefined cell subset were identified.Among them,the two subsets of smooth muscle cells were contractile and secretory,respectively.The results of scRNA-seq indicated that enzymatic hydrolysis with GEXSCOPE kit produced a large number of endothelial cells (57.46%) and a small number of immune cells (13.21%).However,immune cells (34.64%) were dominant in the cells obtained by enzymatic hydrolysis with self-made digestive liquid. Conclusion scRNA-seq can be employed to explore the cellular heterogeneity of diseased vessels in TA patients.Different enzymatic digestion protocols may impact the proportion of different cells.

Single-cell RNA sequencing deciphers transcriptional profiles of hepatocytes in mouse with hepatic alveolar echinococcosis / 中国血吸虫病防治杂志

Objective To investigate the cell composition and the transcriptional characteristics in microenvironments of hepatic tissues in mice at late stage of Echinococcus multilocularis infection at a single-cell level. Methods Peri-lesion and paired distal hepatic specimens were collected from two BALB/c mice (6 to 8 weeks old) infected with E. multilocularis for single-cell RNA sequencing. The Seurat package in the R software was employed for quality control of data, multi-sample integration and correction of batch effects, and uniform manifold approximation and projection (UMAP) algorithm was used for cell clustering. Cell types were annotated using classical marker genes. Differentially expressed genes were screened in each cell type through differential gene expression analysis, and the biological roles of cells were predicted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results A total of 43 710 cells from peri-lesion and distal hepatic tissues of E. multilocularis-infected mice were analyzed, and were classified into 11 cell types, including neutrophils, T cells, macrophages, granulocyte-monocyte progenitor cells, B cells, plasma cells, basophils, hepatic stellate cells, endothelial cells, hepatocytes, and platelets. T cells were the largest population of immune cells in the microenvironment of hepatic tissues, including five CD4+ T cell subsets, two CD8+ T cell subsets and phosphoantigen-reactive γδT cells. The proportions of CD4+ helper T cells and cytotoxic CD4+ T cells decreased and the proportion of T helper 2 (Th2) cells increased in peri-lesion tissues relative to distal hepatic tissues. In addition, the differentially expressed genes in Th2 cells were associated with negative regulation of the immune system, and the highly expressed genes in cytotoxic CD4+ T cells correlated with activation of the immune system. Conclusions Single-cell RNA sequencing deciphers the cell composition and distribution in microenvironments of hepatic tissues from mice infected with E. multilocularis, and the increased proportion of Th2 cells in peri-lesion hepatic tissues may be associated with formation of immunosuppressive microenvironments.

Single cell RNA sequencing technology applicated for drug discovery / 药学学报

Single cell RNA sequencing (scRNA-seq) is an advanced technology to study the transcriptome information at the single cell level. The application of this technology can attribute to analyze the heterogeneous map of cells in the process of disease development, and precisely identify the specific cell subsets that are responsive to pharmacological therapy. Currently, scRNA-seq technology has been widely applied in the field of drug research, including studies on therapeutic targets, drug-induced adverse reactions, drug resistance and vaccine. This work reviews the application of scRNA-seq technology in drug discovery, which offers a scientific basis for personalized and accurate medication therapy.

Advances in single-cell RNA sequencing in the retina / 中华眼底病杂志

Retina is composed of a heterogeneous population of cell types, each with a unique biological function. Even if the same type of cells, due to genetic heterogeneity will lead to cell function differences. In the past, traditional molecular biological methods cannot resolve variations in their functional roles that arise from these differences, and some cells are difficult to define due to the lack of specific molecular markers or the scarcity of numbers, which hindered the understanding and research of these cells. With the development of biotechnology, single-cell RNA sequencing can analyze and resolve differences in single-cell transcriptome expression profiles, characterize intracellular population heterogeneity, identify new and rare cell subtypes, and more definitely define the characteristics of each cell type. It clarifies the origin, function, and variations in cell phenotypes. Other attributes include pinpointing both disease-related characteristics of cell subtypes and specific differential gene expression patterns, to deepen our understanding of the causes and progression of diseases, as well as to aid clinical diagnosis and targeted therapy.

Changes in metabolic capacity and gene expression of brown adipose tissue in the first and third trimester of pregnancy / 中华内分泌代谢杂志

Objective:To explore gene expression and metabolic capacity changes of brown adipose tissue(BAT)during different gestation periods.Methods:A normal pregnancy model was established using C57BL/6J mice, while infertile mice of the same age were served as the control group. The morphological alteration of BAT during pregnancy as well as the gene expression of uncoupling protein 1(UCP1) and other fat browning and mitochondrial marker genes were detected. Moreover, BATs from early and late gestation were selected to screen differentially expressed genes in relation to pregnancy progressing by RNA sequencing(RNA-seq), and gene ontology(GO) and Kyoto gene and gene sequencing(KEGG)were performed.Results:With pregnancy progressing, the size of BAT lipid droplets was substantially enlarged, UCP1 protein expression was decreased( P<0.01), and the fat browning marker genes(Ucp1, Dio2, and Pgc1α)and the mitochondrial marker gene CytC were downregulated( P<0.001). Additionally, a total of 1 298 distinct genes were identified by RNA-seq, 906 of which were upregulated and 392 were downregulated at later stage of pregnancy. GO and KEGG analyses revealed that the differentially expressed genes were mainly enriched in bioregulatory functional pathways such as lipid metabolism, sex steroid hormones, and inflammatory factors. Conclusion:BAT in mice showed larger lipid droplets and reduced thermogenic and metabolic capacity during late gestation, and BAT gene expression was significantly different in different periods of gestation, so reduced metabolic capacity of BAT may contribute to metabolic abnormality during pregnancy.

Application of single cell RNA sequencing in the treatment of diabetes / 中华内分泌代谢杂志

Single-cell RNA sequencing (scRNA-seq) is used for transcriptome profiling at the individual cell level, which is capable of screening in differentially gene expression that results from genetic mutation. Islet-based developmental atlas and heterogeneity characterization are currently the main applications of scRNA-seq in diabetes. scRNA-seq also can be used to mark and purify the functional β cells from resident adult stem cells in the pancreatic islets, which is expected to improve the outcome of islet β cells transplantation in type 1 diabetic patients. In addition, the technique can aid in learning diabetic β cell dedifferentiation and immunomodulatory functions. Although the study of scRNA-seq in diabetic retinopathy, nephropathy, atherosclerosis, and peripheral neuropathy is still at a nascent stage, scRNA-seq has great potential in a wide range of biomedical and clinical applications.

Advances in single-cell RNA sequencing for Kawasaki disease / 国际儿科学杂志

Kawasaki disease, an acute self-limited systematic vasculitis, predominantly affects children under 5 years old.One of the most common complications is coronary artery lesions.Currently, the pathogenesis mechanism of Kawasaki disease is considered to be multifactorial, including genetic susceptibility, impaired immune response, inflammatory injury and so on.Over the past decade, by interpreting the unique gene expression pattern on single-cell level, single-cell RNA sequencing is able to identify new or rare cell subsets and construct cell trajectories.These applications are widely applied to researches of cardiovascular diseases.This review summarizes the development of single-cell RNA sequencing and its applications in researches of the pathogenesis of Kawasaki disease, including animal model and acute phase of Kawasaki disease.

Macrophage differential genes and their functions in silicosis based on single cell RNA sequencing and spatial transcriptome sequencing / 环境与职业医学

Background The rise of single cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing technologies has allowed for intensive study of lung diseases, but both have been poorly studied in silicosis. Objective To explore differentially expressed genes DEGs in silicosis macrophages by scRNA-seq combined with spatial transcriptome sequencing and analyze the potential diagnostic genes. Methods Male C57BL/6 mice (5-6 weeks old, 22-30 g) were randomly divided into 4 groups: normal saline (NS) group for 7 d, NS group for 56 d, SiO2 group for 7 d, and SiO2 group for 56 d, with 1 mouse in each group. A silicosis model was constructed by tracheal drip injection of SiO2 suspension (0.2 g·kg−1, 50 g·cm−2), and the control mice were given the same volume of NS. The right lung was removed for scRNA-seq and the left lung for spatial transcriptome sequencing on day 7 and day 56, respectively. Cell populations were captured using principal component analysis techniques and dimensionality reduction of uniform manifold approximation and projection. The Find Markers function in R language was applied to analyze the DEGs changes of macrophages in two groups of lung tissues, and the corresponding DEGs were subjected to Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes signaling pathway analysis, while STRING and CytoHubba plug-ins of Cytoscape software were applied to protein-protein interaction network analysis to screen out key (Hub) genes. Spatial transcriptome sequencing was used to explore the original location of Hub genes on lung tissue sections and their mapping in lung macrophages. Finally, the correlation of Hub gene expression levels in lung tissues of silicosis patients and mouse silicosis models was verified, the diagnostic efficacy of Hub gene using subject operating characteristic curves (ROC). In vitro experiments by applying cell viability assay were conducted to verify the changes in viability of mouse macrophages (RAW264.7) under SiO2 stimulation. Results The scRNA-seq revealed a total of 20 clusters captured and defined. The results of scRNA-seq and spatial transcriptome sequencing showed an increased number of macrophages in the lung tissue of the SiO2 group compared to the NS group and clustered in the focal areas. Among the 97 macrophage DEGs screened out, 75 were up-regulated genes, and mainly enriched in chemotaxis and migration of neutrophils, chemokine receptor binding, tumor necrosis factor signaling pathway, cytokine-cytokine receptor interaction pathway, and interleukin-17 signaling pathway; and 22 were down-regulated genes, and mainly enriched in late endosomes, peroxisome proliferator-activated receptors signaling pathway, and alcoholic liver disease signaling pathway. A total of 2 core modules and 3 Hub genes were screened out, including Ccl2, Ccl7, and Ptgs2. The scRNA-seq showed that they were expressed at elevated levels in the SiO2 group compared to the NS group and clustered in additional macrophages, and the spatial transcriptome sequencing showed that they clustered in inflammatory areas with nodular lesions. The CCL7 and PTGS2 expressions were increased in the lung tissue of SiO2 patients compared with the healthy subjects, and the areas under the working curve of the subjects were 0.850 and 0.786, respectively. The viability of RAW264.7 cells was enhanced under SiO2 stimulation at 3 h, 6 h, and 12 h compared to those without the stimulation (P<0.05). Conclusion Bioinformatics screening have identified 3 Hub genes (Ccl2, Ccl7, and Ptgs2)and 2 potential diagnostic genes (CCL7 and PTGS2) in the lung tissue of silicosis mice, which may be potential molecular markers of early-stage silicosis with implications for the development and prognosis of silicosis.

Research Progress of Single-cell Transcriptome Sequencing in Immune Microenvironment of Nasopharyngeal Carcinoma / 肿瘤防治研究

We analyze the recent research progress of single-cell transcriptome sequencing of nasopharyngeal carcinoma (NPC), dissect its tumor immune microenvironment, and focus on the role of myeloid cells, T cells, B cells, NK cells, and fibroblasts in the mechanism of action in NPC tissues to provide reference for the diagnosis, treatment, and prognosis prediction of NPC.

Identification of core genes related to severity of respiratory syncytial virus bronchiolitis based on RNA sequencing data / 中华微生物学和免疫学杂志

Objective:To identify the core genes related to the disease severity of respiratory syncytial virus (RSV) bronchiolitis in children using RNA sequencing (RNA-seq) and weighted gene co-expression network analysis (WGCNA), aiming to provide reference for predicting the condition of RSV infection.Methods:Twenty-two patients admitted to the Second Affiliated Hospital of Wenzhou Medical University with RSV bronchiolitis from October 1, 2019 to February 29, 2020 were enrolled as the case group. They were divided into three groups based on the severity of the disease: mild group, moderate group and severe group. Twenty-two healthy children were selected as the control group. Total RNA was extracted from whole blood leukocytes and analyzed by RNA-seq to compare the differentially expressed genes (DEGs) between children with RSV bronchiolitis and healthy children. The gene co-expression modules related to disease severity and biological indicators for disease severity assessment were identified.Results:The median age of the 22 patients (19 males and 3 females) was 3 months. The median age of the 22 healthy children (14 males and 8 females) was 4 months. There was no significant difference in age or gender between the two groups. There were 8 cases in the mild group, 7 cases in the moderate group and 7 cases in the severe group. Through significance analysis, 416 DEGs were found in the mild group, 586 in the moderate group and 846 in the severe group. According to WGCNA analysis, 10 co-expression modules were found, among which brown module ( r=0.62, P<0.001) was significantly correlated with disease severity. The protein-protein interaction network of DEGs in brown module was constructed and the top 30 core genes were selected according to the connectivity of gene nodes, among which the genes with high correlation were RBX1 and PSMA7. The expression of RBX1 and PSMA7 genes was up-regulated in the severe group, but their expression in the mild and moderate groups was not significantly different from that in the control group. Conclusions:RBX1 and PSMA7 genes might be biological predictors of disease severity in RSV bronchiolitis.

Transcriptomics in atopic dermatitis / 中华皮肤科杂志

With the development of transcriptomic technologies such as gene chip technology and RNA sequencing technology, important related factors in the pathogenesis of atopic dermatitis (AD) have been gradually identified, such as different T helper (Th) cell subtypes and other immune-related cells (macrophages and Langerhans cells) ; abnormal changes in active substances such as interleukin-4, interleukin-13, fillagrin and loricrin released by immune-related cells such as Th2 cells and keratinocytes have been found to play major roles in pruritus and skin barrier damage in AD. In recent years, transcriptomic technologies have been applied to the analysis of changes in transcriptomic profiles of patients before and after treatment to evaluate patients′ condition and therapeutic effect. This review summarizes research progress in transcriptomics in AD in recent years.

Application of Single-cell RNA Sequencing Technology to Exploring Cardioprotective Mechanism of Chinese Medicine After Myocardial Infarction： A Rewiew / 中国实验方剂学杂志

The pathological changes of the heart after myocardial infarction （MI） are complex， involving multiple molecular mechanisms and various cells， such as myocardial cells， endothelial cells， fibroblasts， and macrophages. With multiple targets， Chinese medicine demonstrates ideal cardioprotective effect. However， the complex mechanism of multi-component Chinese medicine formulas has not been elucidated， thus limiting the further application. The high-throughput single-cell RNA sequencing （scRNA-seq） technology offers single-cell transcriptome analysis of hundreds of drugs under different processing conditions in a single experiment and identifies the differences in the response of different cells and cell subtypes to drug treatment. scRNA-seq technology helps us to understand the exact cellular and molecular mechanisms of cardiac remodeling from acute ischemic events to chronic cardiac scarring. The application of scRNA-seq to studying the cardioprotective mechanism of Chinese medicine after MI can boost the development of Chinese medicine， help obtain richer， more accurate and comprehensive information. It can give us a clear insight into the mechanism of Chinese medicine based on complex network. In this study， we summarized the research on cardioprotective mechanism of Chinese medicine and introduced the development of scRNA-seq technology and the application to MI research. Finally， we explored the possible application prospects of scRNA-seq in the research on cardioprotective mechanism of Chinese medicine after MI， hoping to provide ideas for the modernization of Chinese medicine.

Single-cell transcriptome analysis of T cells in thyroid and peripheral blood of patients with Hashimoto′s thyroiditis / 中华内分泌代谢杂志

Objective:To construct single-cell transcription landscape of T cell in peripheral blood mononuclear cells(PBMCs) and thyroid tissue of patients with Hashimoto ′s thyroiditis(HT), and to analyze the changes in the proportion and functionality of T cell clusters in HT disease state.Methods:Single cell RNA sequencing was performed on PBMCs and thyroid tissue from 5 HT patients. Single cell RNA sequencing data of PBMCs from 5 healthy individuals were retrieved from public databases. After preliminary clustering, the clusters expressing CD3E were extracted and clustering again, and the names of each cluster were determined according to the known cell markers. The proportion of each cell subtype was compared, and the differentially expressed genes in different samples were analyzed.Results:After quality control, the 71 533 T cells were classified into 19 cell clusters. Among them, the proportion and function of C1_CD4 + Naive T cell clusters, C3_CD4 + Treg cell clusters, C7_CD8 + Naive T cell clusters, C8_GNLY -CD8 + T cell clusters, C10_RORC + CD8 + T cell clusters, C11_ GZMK + CD8 + T cell clusters, C12_CCL4 + CD8 + T cell clusters, and C18_PTGDS + NK cell clusters in thyroid tissue of HT patients were significantly different from those in PBMCs of healthy controls and HT patients. Conclusion:The proportion of multiple T cells in thyroid tissue of HT patients were significantly different from those in PBMCs. Among them, the proportion of three of CD8 + T cell subsets with high expression of cell killing-related genes in thyroid tissue T cells of HT patients is higher than that in PBMCs T cells, and it is statistically significant. In addition, the functionality of various T cells in the thyroid tissue of HT patients are also significantly different from those in PBMCs. A cluster of GZMK + CD8 + T cells showes significantly lower expression of genes related to PD1 pathway in thyroid tissues of HT patients compared with cells in PBMCs of HT patients, also a cluster of CCL4 + CD8 + T cells showes significantly lower expression of genes related to IL-12 pathway.