San-Huang-Yi-Shen Capsule Ameliorates Diabetic Nephropathy in Rats Through Modulating the Gut Microbiota and Overall Metabolism

San-Huang-Yi-Shen capsule (SHYS) has been used in the treatment of diabetic nephropathy (DN) in clinic. However, the mechanisms of SHYS on DN remain unknown. In this study, we used a high-fat diet (HFD) combined with streptozotocin (STZ) injection to establish a DN rat model. Next, we used 16S rRNA sequencing and untargeted metabolomics to study the potential mechanisms of SHYS on DN. Our results showed that SHYS treatment alleviated the body weight loss, hyperglycemia, proteinuria, pathological changes in kidney in DN rats. SHYS could also inhibite the oxidative stress and inflammatory response in kidney. 16S rRNA sequencing analysis showed that SHYS affected the beta diversity of gut microbiota community in DN model rats. SHYX could also decrease the Firmicutes to Bacteroidetes (F to B) ratio in phylum level. In genus level, SHYX treatment affected the relative abundances of Lactobacillus, Ruminococcaceae UCG-005, Allobaculum, Anaerovibrio, Bacteroides and Candidatus_Saccharimonas. Untargeted metabolomics analysis showed that SHYX treatment altered the serum metabolic profile in DN model rats through affecting the levels of guanidineacetic acid, L-kynurenine, prostaglandin F1α, threonine, creatine, acetylcholine and other 21 kind of metabolites. These metabolites are mainly involved in glycerophospholipid metabolism, tryptophan metabolism, alanine, aspartate and glutamate metabolism, arginine biosynthesis, tricarboxylic acid (TCA) cycle, tyrosine metabolism, arginine and proline metabolism, arginine and proline metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and D-glutamine and D-glutamate metabolism pathways. Spearman correlation analysis showed that Lactobacillus, Candidatus_Saccharimonas, Ruminococcaceae UCG-005, Anaerovibrio, Bacteroides, and Christensenellaceae_R-7_group were closely correlated with most of physiological data and the differential metabolites following SHYS treatment. In conclusion, our study revealed multiple ameliorative effects of SHYS on DN including the alleviation of hyperglycemia and the improvement of renal function, pathological changes in kidney, oxidative stress, and the inflammatory response. The mechanism of SHYS on DN may be related to the improvement of gut microbiota which regulates arginine biosynthesis, TCA cycle, tyrosine metabolism, and arginine and proline metabolism.

Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes

The members of the Deinococcaceae family have the ability to survive extreme environmental conditions. Deinococcus species have a complex cell envelope composed of L-ornithine containing peptidoglycan. Anabolism of L-ornithine is intrinsically linked to L-lysine and L-arginine biosynthetic pathways. To understand these two pathways, we analyzed the L-lysine and L-arginine pathways using 23 Deinococcus genomes, including D. indicus. We used BLAST-P based ortholog identification using D. radiodurans genes as the query. We identified some BLAST-P hits that shared the same functional annotation. We analyzed three (class I aminotransferase, acetyl-lysine deacetylase, and acetyl glutamate/acetyl aminoadipate kinase) from L-lysine biosynthesis pathway and three (bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase protein, nitric oxide synthase-like protein, and Acetyl-lysine deacetylase) from L-arginine biosynthesis pathway. Two proteins showed certain structural variations. Specifically, [LysW]-lysine hydrolase protein sequence and structure level changes indicated changes in oligomeric conformation, which could likely be a result of divergent evolution. And, bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase had its active site pocket positions shifted at the structural level and we hypothesize that it may not perform at the optimal level. Thus, we were able to compare and contrast different Deinococcus species indicating some genes occurring because of divergent evolution.

Carbon Ion Radiotherapy Evokes a Metabolic Reprogramming and Individualized Response in Prostate Cancer

Introduction: Carbon ion radiotherapy (CIRT) is a novel treatment for prostate cancer (PCa). However, the underlying mechanism for the individualized response to CIRT is still not clear. Metabolic reprogramming is essential for tumor growth and proliferation. Although changes in metabolite profiles have been detected in patients with cancer treated with photon radiotherapy, there is limited data regarding CIRT-induced metabolic changes in PCa. Therefore, the study aimed to investigate the impact of metabolic reprogramming on individualized response to CIRT in patients with PCa.Materials and Methods: Urine samples were collected from pathologically confirmed patients with PCa before and after CIRT. A UPLC-MS/MS system was used for metabolite detection. XCMS online, MetDNA, and MS-DIAL were used for peak detection and identification of metabolites. Statistical analysis and metabolic pathway analysis were performed on MetaboAnalyst.Results: A total of 1,701 metabolites were monitored in this research. Principal component analysis (PCA) revealed a change in the patient's urine metabolite profiles following CIRT. Thirty-five metabolites were significantly altered, with the majority of them being amino acids. The arginine biosynthesis and histidine metabolism pathways were the most significantly altered pathways. Hierarchical cluster analysis (HCA) showed that after CIRT, the patients could be clustered into two groups according to their metabolite profiles. The arginine biosynthesis and phenylalanine, tyrosine, and tryptophan biosynthesis pathways are the most significantly discriminated pathways.Conclusion: Our preliminary findings indicate that metabolic reprogramming and inhibition are important mechanisms involved in response to CIRT in patients with PCa. Therefore, changes in urine metabolites could be used to timely assess the individualized response to CIRT.

Screening of Altered Metabolites and Metabolic Pathways in Celiac Disease Using NMR Spectroscopy

Background. Celiac disease (CeD) is an autoimmune intestinal disorder caused by gluten protein consumption in genetically predisposed individuals. As biopsy sampling is an invasive procedure, finding novel noninvasive serological markers for screening of at-risk CeD population is a priority. Metabolomics is helpful in monitoring metabolite changes in body fluids and tissues. In the present study, we evaluated serum metabolite levels of CeD patients relative to healthy controls with the aim of introducing new biomarkers for population screening. Method. We compared the serum metabolic profile of CeD patients ( n = 42 ) and healthy controls ( n = 22 ) using NMR spectroscopy and multivariate analysis. Result. 25 metabolites were identified by serum metabolic profiling. Levels of 3-hydroxyisobutyric acid and isobutyrate showed significant differences in CeD patients’ samples compared with healthy controls ( p < 0.05 ). According to pathway analysis, our data demonstrated that changes in nine metabolic pathways were significantly disrupted/affected in patients with CeD. These enriched pathways are involved in aminoacyl-tRNA biosynthesis; primary bile acid biosynthesis; nitrogen metabolism; glutamine and glutamate metabolism; valine, leucine, and isoleucine biosynthesis and degradation; taurine and hypotaurine metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and arginine biosynthesis. Conclusion. In summary, our results demonstrated that changes in the serum level of 25 metabolites may be useful in distinguishing CeD patients from healthy controls, which have the potential to be considered candidate biomarkers of CeD.

Novel Metabolic Biomarker for Early Detection and Prognosis to the Patients with Gastric Cardia Adnocarcinoma

Background: Gastric cardia adenocarcinoma (GCA), which has been normalized as type II of adenocarcinoma at esophagogastric junction in western countries. In clinical, most of the GCA patients are lack of early alarming symptoms, more than 90% of GCA patients were diagnosed at advanced stage, resulted in a very poor prognosis, with less than 20% of 5-year survival. Obviously, early detection for GCA plays crucial role in decreasing the high mortality. Metabolomics allows for appraisal of small molecular mass compounds in a biofluid, which may provide a way for finding biomarkers for GCA. Methods: The serum metabolic features of 276 curatively resected GCA patients and 588 healthy control participates were collected from the database of State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital of Zhengzhou University to discover the metabolic dysregulation by using the ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). Joint pathway analysis with metabolites identified, survival analysis and auxiliary diagnosis metabolites were discussed in present work. Results: A sum of 200 known differential metabolites were obtained with p＜0.05 and fold change FC≥1.25 or FC≤0.8 by comparison GCA and healthy control participates. 12 metabolites significant correlated with survival (p＜0.05) and 17 metabolites for potential auxiliary diagnosis(FC＞1.5 or FC＜0.67) for GCA. Dysregulated arginine biosynthesis was an important pathway of GCA. 9 differential metabolites of 12-ketolithocholic acid, 2-Hydroxybutanoic acid, Aldosterone, All-trans-13,14-dihydroretinol, Hododeoxycholic acid, L-histidine, Malonic acid, Prostaglandin E2 and Sphingosine were identified as potential metabolic markers for distinguishing the GCA and healthy control (AUC=0.976, sensitivity =0.913, specificity =0.027, optimal cut off value=0.470). Conclusions: This work was first identified 12 metabolites significant correlated with survival and 17 metabolites for potential auxiliary diagnosis for GCA. In addition, arginine biosynthesis pathway metabolism showed important roles in GCA. Results provide the understanding of the molecular difference between GCA and healthy control. The novel plasma biomarkers panel could clearly distinguish GCA patients from the healthy control group. This finding may form the basis for the development of a minimally invasive method for GCA detection.

Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model

Background Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear. Results By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a d-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes. Conclusions This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules.

Carbon-ion Evokes Metabolic Reprogramming and Individualized Response in Prostate Cancer

Background: Carbon ion radiotherapy (CIRT) is a novel and powerful tool for prostate cancer (PCa). However, the underlying mechanism for individualized treatment response after CIRT was not clear, and there was still no effective indicator to timely demonstrate the treatment response. Metabolic reprogramming is one of the main hallmarks of malignancy. Metabolic status might have a high relationship with the radiosensitivity and the individualized radiation response. The significant changes of metabolites profiles were detected after radiotherapy in the serum sample of different malignancies. But there was limited data regarding CIRT induced metabolic changes in prostate cancer. Our aim was to preliminary investigate the carbon-ion induced metabolic reprogramming in PCa patients and the individualized response of PCa patients to carbon ion. Methods: Urine samples collected from 15 pathology confirmed PCa patients before and after CIRT were enrolled into this analysis. High-throughput UPLC-MS/MS system was used for metabolites detection. XCMS online, MetDNA and MSDIAL were used for peak detection and identification of metabolites. Statistical analysis and metabolic pathway analysis were performed on Metaboanalyst.Results: A total of 1701 metabolites were monitored by high-throughput UPLC-MS/MS and 217 metabolites were identified. The PCA scores plot revealed clear discrimination of the patient’s urine metabolites profiles before (pre-CIRT) and after (pre-CIRT) CIRT treatment. 35 metabolites significantly altered after CIRT, and these metabolites mainly were amino acid. Pathway enrichment analysis further identified these metabolites could be enriched in 8 pathways (FDR<0.05, impact>2), while arginine biosynthesis and histidine metabolism pathways were the most significant. In addition, the HCA shows that after CIRT, the patients can be clustered into two groups according to the metabolites profiles. The discriminatory metabolites after CIRT in patients urine mainly enriched in the pathway of arginine biosynthesis and phenylalanine, tyrosine, and tryptophan biosynthesis. Conclusion: Metabolic reprogramming and metabolic inhibition seems one of the most important mechanisms of CIRT to cure PCa. Urine metabolites also showed their potentials to timely identify the individualized response of PCa patients to CIRT.

Extensive Metabolite Profiling in the Unexploited Organs of Black Tiger for Their Potential Valorization in the Pharmaceutical Industry

Black tiger (Kadsura coccinea (Lem.)) has been reported to hold enormous pharmaceutical potential. The fruit and rhizome of black tiger are highly exploited in the pharmaceutical and other industries. However, the most important organs from the plant such as the leaf and stem are considered biowastes mainly because a comprehensive metabolite profile has not been reported in these organs. Knowledge of the metabolic landscape of the unexploited black tiger organs could help identify and isolate important compounds with pharmaceutical and nutritional values for a better valorization of the species. In this study, we used a widely targeted metabolomics approach to profile the metabolomes of the K. coccinea leaf (KL) and stem (KS) and compared them with the root (KR). We identified 642, 650 and 619 diverse metabolites in KL, KS and KR, respectively. A total of 555 metabolites were mutually detected among the three organs, indicating that the leaf and stem organs may also hold potential for medicinal, nutritional and industrial applications. Most of the differentially accumulated metabolites between organs were enriched in flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, arginine and proline metabolism, arginine biosynthesis, tyrosine metabolism and 2-oxocarboxylic acid metabolism pathways. In addition, several important organ-specific metabolites were detected in K. coccinea. In conclusion, we provide extensive metabolic information to stimulate black tiger leaf and stem valorization in human healthcare and food.

Integrated Metabolomics and Transcriptomics Analysis of Monolayer and Neurospheres from Established Glioblastoma Cell Lines

Altered metabolic processes contribute to carcinogenesis by modulating proliferation, survival and differentiation. Tumours are composed of different cell populations, with cancer stem-like cells being one of the most prominent examples. This specific pool of cells is thought to be responsible for cancer growth and recurrence and plays a particularly relevant role in glioblastoma (GBM), the most lethal form of primary brain tumours. Here, we have analysed the transcriptome and metabolome of an established GBM cell line (U87) and a patient-derived GBM stem-like cell line (NCH644) exposed to neurosphere or monolayer culture conditions. By integrating transcriptome and metabolome data, we identified key metabolic pathways and gene signatures that are associated with stem-like and differentiated states in GBM cells, and demonstrated that neurospheres and monolayer cells differ substantially in their metabolism and gene regulation. Furthermore, arginine biosynthesis was identified as the most significantly regulated pathway in neurospheres, although individual nodes of this pathway were distinctly regulated in the two cellular systems. Neurosphere conditions, as opposed to monolayer conditions, cause a transcriptomic and metabolic rewiring that may be crucial for the regulation of stem-like features, where arginine biosynthesis may be a key metabolic pathway. Additionally, TCGA data from GBM patients showed significant regulation of specific components of the arginine biosynthesis pathway, providing further evidence for the importance of this metabolic pathway in GBM.