Integrative metagenomic, transcriptomic, and proteomic analysis reveal the microbiota-host interplay in early-stage lung adenocarcinoma among non-smokers.

BACKGROUND: The incidence of early-stage lung adenocarcinoma (ES-LUAD) is steadily increasing among non-smokers. Previous research has identified dysbiosis in the gut microbiota of patients with lung cancer. However, the local microbial profile of non-smokers with ES-LUAD remains largely unknown. In this study, we systematically characterized the local microbial community and its associated features to enable early intervention. METHODS: A prospective collection of ES-LUAD samples (46 cases) and their corresponding normal tissues adjacent to the tumor (41 cases), along with normal lung tissue samples adjacent to pulmonary bullae in patients with spontaneous pneumothorax (42 cases), were subjected to ultra-deep metagenomic sequencing, host transcriptomic sequencing, and proteomic sequencing. The obtained omics data were subjected to both individual and integrated analysis using Spearman correlation coefficients. RESULTS: We concurrently detected the presence of bacteria, fungi, and viruses in the lung tissues. The microbial profile of ES-LUAD exhibited similarities to NAT but demonstrated significant differences from the healthy controls (HCs), characterized by an overall reduction in species diversity. Patients with ES-LUAD exhibited local microbial dysbiosis, suggesting the potential pathogenicity of certain microbial species. Through multi-omics correlations, intricate local crosstalk between the host and local microbial communities was observed. Additionally, we identified a significant positive correlation (rho > 0.6) between Methyloversatilis discipulorum and GOLM1 at both the transcriptional and protein levels using multi-omics data. This correlated axis may be associated with prognosis. Finally, a diagnostic model composed of six bacterial markers successfully achieved precise differentiation between patients with ES-LUAD and HCs. CONCLUSIONS: Our study depicts the microbial spectrum in patients with ES-LUAD and provides evidence of alterations in lung microbiota and their interplay with the host, enhancing comprehension of the pathogenic mechanisms that underlie ES-LUAD. The specific model incorporating lung microbiota can serve as a potential diagnostic tool for distinguishing between ES-LUAD and HCs.

[Bioinformatics database and production layout visual analysis platform of medicinal plants:a case study of Dao-di medicinal materials in Sichuan province].

In the new stage of trans-omics and trans-subjects for medicinal plants, it is an urgent need to integrate big data, provide interactive applications, and form a unified and multi-level research system and big data platform. Dao-di medicinal material, as an important source of medicinal plants, is a unique quality concept and comprehensive standard of tranditional Chinese medicine(TCM). Several databases have been developed in China and abroad, such as the Encyclopedia of Traditional Chinese Medicine(ETCM) and the Global Pharmacopoeia Genome Database(GPGD). Yet, most databases do not provide multi-dimensional data, including geographic data, phenotype data, compound data, and genetic data. Sichuan, known as the hometown of TCM therapies and the treasure trove of TCM, is the most representative region of medicinal plant diversity in China. According to the latest data of the fourth national survey of TCM resources, there are more than 8 000 TCM and 86 Dao-di medicinal materials in Sichuan province. Based on resource census data and relevant achievements, this study constructed the bioinformatics database of medicinal plants and the visual analysis platform of production layout by taking the Dao-di medicinal materials in Sichuan province as an example, covering geographic data, phenotype data, compound data, and genetic data. It effectively integrates multi-dimensional data of Dao-di medicinal materials and provides different levels of data interaction applications. The platform is the first large-scale multi-dimensional database and visual platform of Dao-di medicinal materials in Sichuan province, which serves as an essential resource for germplasm resources identification, decomposition of biosynthetic pathways, molecular breeding of varieties and provides medicinal plant resource information and data support for development and utilization of medicinal plants in China and abroad.

SARS-Cov-2 spike induces intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9.

Background: Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), as a typical tumor marker, has been found to exert immunomodulatory effects in many diseases. We previously reported the clinical and molecular evidences supporting that SARS-Cov-2 infected the gastrointestinal (GI) tract and found a reduction of CEACAM5 in COVID-19 patients' feces which associated with gut dysbiosis. Yet the role of CEACAM5 in GI infection is ill-defined. Methods: Mice models were established through intraperitoneally injecting with recombinant viral spike-Fc to mimic the intestinal inflammation. We collected duodenum, jejunum, ileum and colon samples after 6h, 2 days, 4 days and 7 days of spike-Fc or control-Fc injection to perform proteomic analysis. Blood was collected from healthy donors and peripheral blood mononuclear cells (PBMC) were separated by density gradient centrifugation, then CD4+ T cells were isolated with magnetic beads and co-cultured with Caco-2 cells. Results: In addition to intestinal CEACAM5, the expression of tight junction and the percent of CD4+ T lymphocytes were significantly decreased in spike-Fc group compared to control (p < 0.05), accompanied with increased level of inflammatory factors. The KEGG analysis revealed differentially expressed proteins were mainly enriched in the coronavirus disease (COVID-19), tight junction, focal adhesion, adherens junction and PI3K-Akt signaling pathway. Protein-protein interaction (PPI) network analysis identified the interaction between CEACAM5 and Galectin-9 that was also verified by molecular docking and co-IP assay. We further confirmed a reduction of CEACAM5 in SARS-CoV-2 spike stimulated enterocytes could promote the expression of Galectin-9 protein in CD4+T cells. Then it gave rise to the increasing release of inflammatory factors and increased apoptosis of CD4+T cells by inhibition of PI3K/AKT/mTOR pathway. Ultimately intestinal barrier dysfunction happened. Conclusion: Our results indicated that CEACAM5 overexpression and Galectin-9 knockdown played a protective role in intestinal barrier injury upon spike-Fc stimulation. Collectively, our findings identified firstly that SARS-CoV-2 spike induced intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. The result provides potential therapeutic targets in intestinal barrier dysfunction for treating severe COVID patients.

Effect of a Self-Assembled Nucleating Agent on the Crystallization Behavior and Spherulitic Morphology of Poly(lactic acid).

Herein, decanedioic acid dibenzoylhydrazide (DDBH) was used as a nucleating agent to improve the crystallization of poly(lactic acid) (PLA). The formation of DDBH assemblies in PLA melts at different concentrations was systematically investigated. The DDBH (0.5-0.9 wt %) recrystallized as dendrite-like structures during the isothermal crystallization process, and the crystal morphology of PLA underwent a morphological change from spherical form to a similar dendritic crystal form. Differential scanning calorimetry and in situ wide-angle X-ray diffraction analysis results showed that crystallizability and overall crystallization rate of PLA were enhanced by the addition of DDBH. The half-crystallization time at 120 °C reduced to 0.28 min compared to pure PLA (6.12 min), after adding 0.9 wt % DDBH. Moreover, the crystallinity and lamellar thickness of crystalline PLA increased, while the size of the microcrystal of PLA decreased with an increase in DDBH content. The heat deflection temperatures of PLA/DDBH blends increased and hence heat resistance improved.

Expression of ACE2, TMPRSS2, and SARS-CoV-2 nucleocapsid protein in gastrointestinal tissues from COVID-19 patients and association with gastrointestinal symptoms.

BACKGROUND: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect the gastrointestinal (GI) tract in coronavirus disease 2019 (COVID-19) patients, the mechanism of GI tract injury is largely unknown. We aimed to study the potential factors that cause COVID-19 GI symptoms. METHODS: We investigated the expression and co-localization of angiotensin converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2), SARS-CoV-2 nucleocapsid protein (NP), and the severity of inflammation in GI tissues from COVID-19 patients (n = 19) by immunofluorescence and histopathologic staining, and then studied their associations with GI symptoms. RESULTS: Infected stomach tissues showed significantly higher ACE2 expression than uninfected ones, while infected duodenum tissues showed significantly higher TMPRSS2 expression than uninfected ones. The expression of TMPRSS2 exhibited a moderate correlation with viral NP across different GI tissues, while no significant association was observed between ACE2 and viral NP. Some GI symptoms such as diarrhea and nausea, were related to the expression level of ACE2, TMPRSS2 or the severity of inflammation. Furthermore, age and elevated aspartate transaminase were major risk factors for disease progression. CONCLUSIONS: ACE2 and TMPRSS2 were essential proteins in the SARS-CoV-2 infection of GI tract, while TMPRSS2 rather than ACE2 may play a more important role. GI symptoms may derive from the host receptor expression level and pro-inflammatory response in COVID-19 patients after viral infection of GI tissues, and further exacerbate the disease. So targeting TMPRSS2 and inflammation may represent an effective strategy for treating COVID-19 patients with GI symptoms.

[Analysis of WRKY transcription factor family based on full-length transcriptome sequencing in Polygonatum cyrtonema].

WRKY transcription factor family plays an important role in plant growth and development, secondary metabolite synthesis, and biotic and abiotic stress responses. The present study performed full-length transcriptome sequencing of Polygonatum cyrtonema by virtue of the PacBio SMRT high-throughput platform, identified the WRKY family by bioinformatics methods, and analyzed the physicochemical properties, subcellular localization, phylogeny, and conserved motifs. The results showed that 30.69 Gb nucleotide bases and 89 564 transcripts were obtained after redundancy removal. These transcripts had a mean length of 2 060 bp and an N50 value of 3 156 bp. Based on the full-length transcriptome sequencing data, 64 candidate proteins were selected from the WRKY transcription factor family, with the protein size of 92-1 027 aa, the relative molecular mass of 10 377.85-115 779.48 kDa, and the isoelectric point of 4.49-9.84. These WRKY family members were mostly located in the nucleus and belonged to the hydrophobic proteins. According to the phylogenetic analysis of WRKY family in P. cyrtonema and Arabidopsis thaliana, all WRKY family members were clustered into seven subfamilies and WRKY proteins from P. cyrtonema were distributed in different numbers in these seven subgroups. Expression pattern analysis confirmed that 40 WRKY family members had distinct expression patterns in the rhizomes of 1-and 3-year-old P. cyrtonema. Except for PcWRKY39, the expression of 39 WRKY family members was down-regulated in 3-year-old samples. In conclusion, this study provides abundant reference data for genetic research on P. cyrtonema and lays a foundation for the in-depth investigation of the biological functions of the WRKY family.

pH-sensitive molybdenum (Mo)-based polyoxometalate nanoclusters have therapeutic efficacy in inflammatory bowel disease by counteracting ferroptosis.

Current therapeutic drugs for ulcerative colitis (UC) remained inadequate due to drug dependence and unacceptable adverse events. Reactive oxygen species (ROS) played a critical role in the occurrence and development of UC, which most likely benefited from treatment in scavenging ROS. In this study, we developed a pH-sensitive molybdenum-based polyoxometalate (POM) nanocluster, which might contribute to site specific colonic delivery and enhance systemic efficacy of UC treatment. Our results demonstrated that POM displayed robust ROS scavenging ability in vitro. POM could significantly alleviate the enteric symptoms and inflammatory indicators in DSS-induced UC mouse models. Flow cytometry showed an effective diminishment of macrophages, neutrophils and T cells infiltration after POM administration in UC models. Also, for the first time, we demonstrated that POM interfered with metabolic pathway associated to oxidative stress and partially improved the abnormal production of intestinal metabolites in UC to some extent. Benefiting from the ROS scavenging ability, POM attenuated ferroptosis in DSS induced UC, as evidenced by increase of GSH, down-expression of GPX4 and improvement in mitochondrial morphological changes. Meanwhile, there were no side effects on normal tissues. Thus, our powerful therapeutic effects pioneered the application of POM for safer and more effective POM-based UC therapy.

Understanding the tonifying and the detoxifying properties of Chinese medicines from their impacts on gut microbiota and host metabolism: a case study with four medicinal herbs in experimental colitis rat model.

BACKGROUND: Chinese medicines (CMs) have emerged as an alternative therapy for ulcerative colitis through reinforcing the vital qi and/or eliminating the pathogenic factors according to the traditional Chinese medicinal theory. Presystemic interactions of CMs with gut microbiota and the associated metabolic network shift are believed to be essential to achieve their holistic health benefits in traditional oral application. METHODS: This study first employed 16S rDNA-based microbial profiling and mass spectrometry-based urinary metabolomics to simultaneously evaluate four single CMs frequently prescribed as main constituent herbs for alleviating UC, the tonic ginseng and Astragali Radix (AR) and the detoxifying Scutellaria Radix (SR) and Rhubarb, on a dextran sodium sulfate (DSS)-induced colitis rat model, with aims to understanding the tonifying or detoxifying properties of CMs through clinical phenotypes, the common features and herb-specific signatures in gut microbial alterations and the associated host metabolic shifts. Colitis was induced in rats receiving 5% DSS for consecutive 7 days. Control group received water alone. Herbal groups received 5% DSS and respective herbal preparation by gavage once daily. Body weight, stool consistency, and rectal bleeding were recorded daily. Feces and urine were freshly collected at multiple time points. On day 7, blood and colon tissues were collected to determine anti-/pro-inflammatory cytokines levels, colonic myeloperoxidase activity, and histopathologic alterations. RESULTS: Gut microbiome was more prone to herb intervention than metabolome and displayed increasing associations with metabolic dynamics. Although both the tonic and the detoxifying herbs alleviated colitis and caused some similar changes in DSS-induced microbiome and metabolome disturbance, the tonic herbs were more effective and shared more common microbial and metabolic signatures. The detoxifying herbs elicited herb-specific changes. Rhubarb uniquely affected phenylalanine metabolism and established high correlations between Akkermansia muciniphila and Parasutterella and hydroxyphenylacetylglycine and phenylbutyrylglycine, while SR caused significant elevation of steroidal glucuronides dehydropregnenolone glucuronide and estriol glucuronide, both displaying exclusive correlations with genus Acetatifactor. CONCLUSION: Both tonic and detoxifying herbs tested ameliorated experimental colitis and elicited alternative microbial and host metabolic reprogramming. The findings highlight the importance of presystemic interactions with gut microbiota to host metabolic shifts and promote modern translation of tonic and detoxifying properties of CMs.

Fecal multi-omics analysis reveals diverse molecular alterations of gut ecosystem in COVID-19 patients.

Gut ecosystem has profound effects on host physiology and health. Gastrointestinal (GI) symptoms were frequently observed in patients with COVID-19. Compared with other organs, gut antiviral response can result in more complicated immune responses because of the interactions between the gut microbiota and host immunity. However, there are still large knowledge gaps in the impact of COVID-19 on gut molecular profiles and commensal microbiome, hindering our comprehensive understanding of the pathogenesis of SARS-CoV-2 and the treatment of COVID-19. We performed longitudinal stool multi-omics profiling to systemically investigate the molecular phenomics alterations of gut ecosystem in COVID-19. Gut proteomes of COVID-19 were characterized by disturbed immune, proteolysis and redox homeostasis. The expression and glycosylation of proteins involved in neutrophil degranulation and migration were suppressed, while those of proteases were upregulated. The variable domains of Ig heavy chains were downregulated and the overall glycosylation of IgA heavy chain constant regions, IgGFc-binding protein, and J chain were suppressed with glycan-specific variations. There was a reduction of beneficial gut bacteria and an enrichment of bacteria derived deleterious metabolites potentially associated with multiple types of diseases (such as ethyl glucuronide). The reduction of Ig heave chain variable domains may contribute to the increase of some Bacteroidetes species. Many bacteria ceramide lipids with a C17-sphingoid based were downregulated in COVID-19. In many cases, the gut phenome did not restore two months after symptom onset. Our study indicates widely disturbed gut molecular profiles which may play a role in the development of symptoms in COVID-19. Our findings also emphasis the need for ongoing investigation of the long-term gut molecular and microbial alterations during COVID-19 recovery process. Considering the gut ecosystem as a potential target could offer a valuable approach in managing the disease.

A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.

BACKGROUND: Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn's disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis. RESULTS: We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with ß-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events. CONCLUSIONS: This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance. Video abstract.

Dextran sulfate sodium-induced colitis and ginseng intervention altered oral pharmacokinetics of cyclosporine A in rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Application of cyclosporine A (CsA) as a rescue treatment in acute severe ulcerative colitis (UC) is limited by its narrow therapeutic window and great interpatient variability. As a substrate of cytochrome P450 3A enzyme (CYP3A) and P-glycoprotein (P-gp), the oral pharmacokinetics of CsA is susceptible to disease status and concomitant medications. Combined treatment with ginseng, a famous medicinal herb frequently prescribed for ameliorating abnormal immune response in many diseases including UC, showed immunologic safety in CsA-based immunosuppression. AIM OF THE STUDY: Since the therapeutic levels of CsA can be achieved within 24 h, this study first assessed the impact of acute colitis and ginseng intervention on the single oral dose pharmacokinetics of CsA and explored the underlying mechanisms in dextran sulfate sodium (DSS)-induced colitis rats and Caco-2 cells. MATERIALS AND METHODS: Rats received drinking water (normal group), 5% DSS (UC group), or 5% DSS plus daily oral ginseng extract (GS+UC group). On day 7, GS+UC group only received an oral dose of CsA (5 mg/kg), while animals of normal or UC group received an oral, intravenous (1.25 mg/kg), or intraperitoneal dose of CsA (1.25 mg/kg), respectively. Blood, liver/intestine tissues and fecal samples were collected for determining CsA and main hydroxylated metabolite HO-CsA or measuring hepatic/intestinal CYP3A activity. Caco-2 cells were incubated with gut microbial culture supernatant (CS) of different groups or ginseng (decoction or polysaccharides), and then CYP3A, P-gp and tight junction (TJ) proteins were determined. RESULTS: Oral CsA exhibited enhanced absorption, systemic exposure and tissue accumulation, and lower fecal excretion, while intravenous or intraperitoneal CsA showed lower systemic exposure and enhanced distribution, in colitis rats. Diminished intestinal and hepatic P-gp expression well explained the changes with DSS-induced colitis. Moreover, blood exposures of HO-CsA in both normal and colitis after oral dosing were significantly higher than intravenous/intraperitoneal dosing, supporting the dominant role of intestinal first-pass metabolism. Interestingly, colitis reduced CYP3A expression in intestine and liver but only potentiated intestinal CYP3A activity, causing higher oral systemic exposure of HO-CsA. Oral ginseng mitigated colitis-induced down-regulation of CYP3A and P-gp expression, facilitated HO-CsA production, biliary excretion and colonic sequestration of CsA, while not affected CsA oral systemic exposure. In Caco-2 cells, gut microbial CS from both colitis and GS+UC group diminished P-gp function, while ginseng polysaccharides directly affected ZO-1 distribution and suppressed TJ proteins expression, explaining unaltered oral CsA systemic exposure. CONCLUSIONS: DSS-induced colitis significantly altered oral CsA disposition through regulating intestinal and hepatic P-gp and CYP3A. One-week ginseng treatment enhanced colonic accumulation while not altered the systemic exposure of CsA after single oral dosing, indicating pharmacokinetic compatibility between the two medications.

The impact of new modes of electronic communication in the treatment of severe acute respiratory syndrome coronavirus 2 infection.

BACKGROUND: More than 26,760,000 cases of SARS-CoV-2 infection have been reported globally to date. This study aimed to analyze the impact of new electronic communication tools in the diagnosis and treatment of patients with SARS-CoV-2 infection. METHODS: From January 20 to February 26, 2020, adult patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection who were treated in The Fifth Affiliated Hospital, Sun Yat-sen University, in Zhuhai, China, were recruited. Forty-seven eligible patients were enrolled and randomly classified into either the test group or the control group. All of the patients received the standard therapeutic regimen and routine ward rounds. The test group was subdivided into three subgroups: the first subgroup (5-minute group) was given an extra 5-minute ward round by WeChat voice call once daily for basic disease communication; the second subgroup (10-minute group) received an extra 10-minute ward round by WeChat voice call once daily for further detail; and the third subgroup (20-minute group) was given an extra 10-minute ward round via WeChat voice call once daily, as well as an extra 10 minutes every 3 days. The primary outcome was the duration of positive-to-negative conversion of SARS-CoV-2 nucleic acid diagnosed by the NAT (nucleic acid testing). RESULTS: In the test groups, the median time from diagnosis to the endpoint was 7.0 days [interquartile range (IQR), 3.8-10.8], compared with 10.0 days (IQR, 6.5-14.5) in the control group. It showed significant reduced the duration time of virus from positive to negative by the NAT (nucleic acid testing), (P=0.032) especially between the 10-minute subgroup (3.0 days; IQR, 3.0-7.5) and the control group (P=0.0065). CONCLUSIONS: The use of new modes of electronic communication can benefit patients during the COVID-19 pandemic and could be extremely valuable in addressing the shortage of medical protective equipment and reducing occupational risk of exposure to infection.

Tetrahydrocurcumin ameliorates diabetes profiles of db/db mice by altering the composition of gut microbiota and up-regulating the expression of GLP-1 in the pancreas.

Diabetes is a worldwide healthy concern, which affects approximately 9% of the population. Tetrahydrocurcumin (THC) is the main metabolite of curcumin, which exerts the anti-diabetic activity. However, the underlying mechanism has not been clarified. In the research, we investigated whether THC could improve diabetes by regulating the gut microbiota and the expression of pancreatic glucagon-like peptide-1 (GLP-1) in the db/db mice. After 8-week THC administration (ig., once a day, THCH group: 200 mg/kg, THCL group: 100 mg/kg), the fasting blood glucose (FBG) was measured every two weeks. Serum insulin levels, the expression of GLP-1 in the pancreas, the histopathology of pancreas and the composition of gut microbiota were evaluated at the end of the experiment. Compared to the diabetic group, THC treatment decreased significantly blood glucose, increased the secretion of insulin and the expression of GLP-1 in the pancreas. Histomorphological analysis revealed that THC could protect pancreatic islet cells against hyperglycemic insult. Furthermore, the data from the sequencing of the 16S rDNA genes in gut microbiome displayed that THC could restore the intestinal dysbiosis, including the lowered relative abundance of Proteobacteria, Actinobacteria and the ratio of Firmicutes to Bacteroidetes. The linear regression analysis showed a close correlation between the GLP-1 expression and the proportion of the intestinal microflora. Altogether, these results demonstrated that THC might have a direct regulatory effect on gut microflora, which indirectly decrease the FBG levels by modulating GLP-1 expression in the pancreas.

Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection.

OBJECTIVE: To study the GI symptoms in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients. DESIGN: We analysed epidemiological, demographic, clinical and laboratory data of 95 cases with SARS-CoV-2 caused coronavirus disease 2019. Real-time reverse transcriptase PCR was used to detect the presence of SARS-CoV-2 in faeces and GI tissues. RESULTS: Among the 95 patients, 58 cases exhibited GI symptoms of which 11 (11.6%) occurred on admission and 47 (49.5%) developed during hospitalisation. Diarrhoea (24.2%), anorexia (17.9%) and nausea (17.9%) were the main symptoms with five (5.3%), five (5.3%) and three (3.2%) cases occurred on the illness onset, respectively. A substantial proportion of patients developed diarrhoea during hospitalisation, potentially aggravated by various drugs including antibiotics. Faecal samples of 65 hospitalised patients were tested for the presence of SARS-CoV-2, including 42 with and 23 without GI symptoms, of which 22 (52.4%) and 9 (39.1%) were positive, respectively. Six patients with GI symptoms were subjected to endoscopy, revealing oesophageal bleeding with erosions and ulcers in one severe patient. SARS-CoV-2 RNA was detected in oesophagus, stomach, duodenum and rectum specimens for both two severe patients. In contrast, only duodenum was positive in one of the four non-severe patients. CONCLUSIONS: GI tract may be a potential transmission route and target organ of SARS-CoV-2.

[Transcriptome and quality evaluation of Sichuan Dao-di herbs Zanthoxylum bungeanum].

"Huajiao" is dried ripe fruit peel of Zanthoxylum bungeanum or Z. schinifolium, is konwn as geoherbs, especially the "Dahongpao" cultivated in Hanyuan, Maoxian and Jiulong of Sichuan province. However, the genetic basis of Dao-di "Huajiao" is virtually unknown. The transcriptome of the fruit and leaf from Sichuan(Hanyuan, Jiulong, Lixian, Maoxian), Gansu(Wudu) province and Shaanxi(Fengxian) province was sequenced. Trinity de novo assembling resulted in a total of 177 616 unigenes. Through the KEGG, NR, SwissProt, Trembl, KOG/COG, GO, Pfam database comparision 106 644 annotated Unigene finally, 4 574 deferentially expressed genes were found in fruit between Sichuan and other provinces, including 3 740 up-regulated genes and 834 down-regulated genes. Among the up-regulated genes, 27 up-regulated genes were raleted to terpenoids, and 8 up-regulated genes were related to isoquinoline alkaloid bio-synthesis. Furthermore, it was also showed remarkable differences in groups which enrichment ratio of the diffe-rent expressed gene compared. The different expressed genes were annotated by the KEGG database into plant-pathogen interaction, plant hormone signal transduction and phenylpropanoid biosynthesis in fruit and leaf, but isoflavonoid bio-synthesis and betaine bio-synthesis were significantly different in fruit and leaf. The study laid a certain reference basis for comparison of quality and different expressed gene of Z. bungeanum from different groups.

Egr1 Knockdown Combined with an ACE Inhibitor Ameliorates Diabetic Kidney Disease in Mice: Blockade of Compensatory Renin Increase.

BACKGROUND: Increased compensatory intrarenal renin diminishes the efficacy of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) in the treatment of diabetic kidney disease (DKD). Early growth response-1 (Egr1) is a crucial transcriptional factor in the progress of DKD and is a potential transcription factor of intrarenal renin according to bioinformatic analysis. However, whether inhibition of Egr1 can suppress compensatory renin increase in DKD is unclear. METHODS: We generated a high-fat diet (HFD)/streptozotocin (STZ)-induced diabetic mouse model. The mice were treated with either enalapril (an ACEI) or enalapril combined with a shEgr1 plasmid, and age-matched DKD mice were used as controls. Urine microalbumin, urinary renin and kidney TGF-ß1 were determined by enzyme-linked immunosorbent assay (ELISA). Hematoxylin and eosin (H&E) and Masson staining were used to determine renal pathological changes. Egr1, renin, TNF-α, and FN were measured by real-time quantitative PCR, Western blot, and immunohistochemistry. The SV40-MES13 murine mesangial cell line was transfected with pENTER-Egr1 plasmid and siEgr1. RESULTS: Our results showed that enalapril increased the renin level of urinary and renal in DKD mice, while shEgr1 attenuated this effect. In addition, enalapril treatment reduced the levels of urinary microalbumin, TNF-α, TGF-ß1 and FN, and alleviated the pathological changes, while shEgr1 strengthened these effects. The protein and mRNA expression of renin in the SV40 MES13 cells was upregulated and downregulated following overexpression and silence of Egr1, respectively. CONCLUSION: Silence of Egr1 could alleviate renal injury in DKD by downregulating intrarenal renin.

High-resolution MS/MS metabolomics by data-independent acquisition reveals urinary metabolic alteration in experimental colitis.

INTRODUCTION: Traditional high-resolution MS1 based untargeted metabolomics suffers from low sensitivity, while low-resolution MS/MS based multiple reaction monitoring increases sensitivity at the cost of metabolite coverage and the mass accuracy. OBJECTIVES: To evaluate and apply the high-resolution MS/MS level untargeted metabolomics. METHODS: SWATH based data-independent acquisition (DIA) was optimized to obtain MS/MS of all precursor ions. RESULTS: SWATH-MS/MS could rescue MS1 obscured or saturated metabolites and potentially provide diagnostic fragments to differentiate isomers. For SWATH-MS/MS, 4944 out of 21492 (23.0%) and 2289 out of 12831 (17.8%) fragment ion features significantly changed (Fold change > 1.5, P < 0.05) between Normal and experimental acute ulcerative colitis (UC) groups in positive and negative ion mode, respectively. For SWATH-MS1, 1022 out of 4818 (21.2%) and 353 out of 2266 (15.6%) features significantly changed in positive and negative ion mode, respectively. By deciphering the metabolite profiles with high-resolution MS/MS, it allows versatile post-acquisition data mining such as open detection of different sub-metabolome. The method revealed a global urinary metabolic alteration and increased glucuronide and sulfate sub-metabolome in UC. The major limitation of untargeted SWATH-MS/MS is increased interferences derived from wider Q1 isolation window. CONCLUSIONS: SWATH-MS/MS is a versatile metabolomics strategy, merging the coverage of high-resolution untargeted metabolomics and the sensitivity of MS/MS.

Are personalized tongxie formula based on diagnostic analyses more effective in reducing IBS symptoms?-A randomized controlled trial.

OBJECTIVES: To examine the efficacy and safety ofpersonalized tongxie formulas; to decrease type II errors to minimum. METHODS: Patients were randomized (1:1:1) into three groups given tongxie, placebo, or pinaverium 3 times daily for 4 weeks. Patients in the tongxie group were treated with personalized formulas based on TCM differential diagnosis, i.e., basic type of IBS, IBS due to liver depression and qi stagnation, excess heat in the liver, deficient spleen function, deficient kidney function, and others (groups 1-6). Primary endpoints were significantly greater reductions in abdominal pain and Bristol stool score. Secondary endpoints were reductions in pain and stool frequencies and abdominal discomfort and its frequency. RESULTS: There were significantly more patients whose stool consistencies were improved than pains were relieved in the entire population (p < 0.001), but there was no significantly difference in subpopulation group 3 (p > 0.05). There were significantly more patients whose stool frequencies were reduced than pain frequencies were reduced in the entire population (p < 0.001), but there were no significantly difference in the subpopulation Groups 1, 3, 4, and 6 (p > 0.05). Multiple active ingredients and their mechanisms of actions to relieve IBS symptoms were identified. CONCLUSION: The outcomes in subpopulations may be different from those of the entire population, indicating that personalized formulas are important to achieve optimal outcomes; the active ingredients and innovative mechanisms identified in this study can be the candidates for developing new IBS drugs, and used to manage IBS, respectively. TRIAL REGISTRATION: NCT01641224 (www.ClinicalTrials.gov).

[New method for evaluating pharmacodynamics of traditional Chinese medicine compounds based on its moderate regulation and principle of balanced adjustment of immunity under pan-immunomic].

For the basic research on the traditional Chinese medicine(TCM), objective syndrome of traditional Chinese medicine and evaluation criteria of traditional Chinese medicine compounds are hardly to break though. While, the modern immunology points out that the body is a counterbalance state and immune imbalance is the root of sickness. The thinking mode of treating diseases in traditional Chinese medicine is also "balance", considering disease is the result of bias which present the imbalance of "Yin counters Yang", "exterior counters interior", "cold counters heat" and "weak counters strong". The Chinese herbal compound formula preparation was applied on disease therapy based on theory of Chinese medicine, which was confirmed by long period clinical application. It is composed of multi-compounds and has the characteristic of multi-targeting. Integrative medicine has spawned pan-immunomics, and the evaluation of immune function (immune balance) has become an important basis for diagnosis and treatment models of integrative medicine. In addition, balance is the core idea of whole-systemic conception of traditional Chinese medicine. Therefore, we speculate that immune balance under pan-immunomic can bridge the traditional Chinese medicine and modern integrative medicine and is the important basis for objective syndrome of traditional Chinese medicine and evaluation criteria of traditional Chinese medicine compounds. According to the bridging theory, we attempt to utilize informatics and statistical methods to construct an evaluation system for pharmacodynamics of traditional Chinese medicine based on its moderate regulation and the balanced adjustment of immunity under pan-immunomic, which further reveal the scientific essence of the whole-systemic view of traditional Chinese medicine. This research brings out a new valuable strategy and provides a theoretical basis for accelerating the transformation of traditional Chinese medicine, especially the exploitation of Chinese herbal compound formula, and constructing the new drug innovation and review system for traditional Chinese medicine. Besides as a reference for traditional Chinese medicine objective syndrome and pharmacodynamics of traditional Chinese medicine compounds, the evaluation system can screen the immunity of sub-health population also. With the continuous accumulation of clinical sample and data, the evaluation system will be more accurate and intelligent.