Amino Acid Metabolism-related Genes Research Articles

Fecal Microbial Changes in Response to Finishing Pigs Directly Fed With Fermented Feed.

The present study investigated the effects of fermented complete feed (FCF) on fecal microbial composition during the grower-finisher period. A total of 20 pigs (Duroc × Landrace × Yorkshire, 48.74± 1.49 kg) were divided randomly into two groups: the CN group (pigs fed with a basal diet) and the FCF group (pigs fed with FCF). After a 60-day trial period, 3 pigs with middle-weight from each treatment were selected for fecal sampling and fecal microbiota analysis. The results showed that the FCF significantly increased operational taxonomic units (OUT) numbers, alpha diversity (Simpson index and Shannon index), and beta diversity, which means that FCF increased the fecal microbiota diversity. At the phylum level, the abundance of Tenericutes, Spirochaetae, Verrucomicrobia, and Cyanobacteria were changed in pigs fed with FCF; and at the genus level, the abundance of Christensenellaceae_R-7_group, Treponema_2, Ruminococcaceae_UCG-005, Prevotellaceae_UCG-003, Phascolarctobacterium, Roseburia, and Prevotella_9 were changed in pigs fed with FCF. The linear discriminant analysis effect size (LEfSe) analysis showed that Roseburia and Prevotella_9 genera were increased, while Tenericutes phyla and Streptococcus, Christensenellaceae_R-7_group, and Lactobacillus genera were decreased in the FCF group compared to the CN group. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) results predicted that the relative abundance of infectious diseases: parasitic associated genes, xenobiotics biodegradation, and metabolism-associated genes were significantly reduced in the FCF group when compared with the CN group, and the relative abundance of signal transduction associated genes, amino acid metabolism-related genes, and replication and repair associated genes were significantly higher in the FCF group when compared with the CN group. In addition, the relative abundance of transport and catabolism-associated genes, membrane transport-associated genes, and biosynthesis of other secondary metabolite-associated genes tended to be higher in the FCF group when compared with the CN group; and the relative abundance of immune diseases associated genes tended to be lower in the FCF group when compared with the CN group. In conclusion, the FCF influenced the alpha and beta diversity of the fecal microbiota of pigs.

A Prognostic Model for Colon Adenocarcinoma Patients Based on Ten Amino Acid Metabolism Related Genes

BackgroundAmino acid metabolism plays a vital role in cancer biology. However, the application of amino acid metabolism in the prognosis of colon adenocarcinoma (COAD) has not yet been explored. Here, we construct an amino acid metabolism-related risk model to predict the survival outcome of COAD and improve clinical decision making.MethodsThe RNA-sequencing-based transcriptome for 524 patients with COAD from The Cancer Genome Atlas (TCGA) was selected as a training set. The integrated Gene Expression Omnibus (GEO) dataset with 1,430 colon cancer samples was used for validation. Differential expression of amino acid metabolism-related genes (AAMRGs) was identified for prognostic gene selection. Univariate cox regression analysis, LASSO-penalized Cox regression analysis, and multivariate Cox regression analysis were applied to construct a prognostic risk model. Moreover, the correlation between risk score and microsatellite instability, immunotherapy response, and drug sensitivity were analyzed.ResultsA prognostic signature was constructed based on 10 AAMRGs, including ASPG, DUOX1, GAMT, GSR, MAT1A, MTAP, PSMD12, RIMKLB, RPL3L, and RPS17. Patients with COAD were divided into high-risk and low-risk group based on the medianrisk score. Univariate and multivariate Cox regression analysis revealed that AAMRG-related signature was an independent risk factor for COAD. Moreover, COAD patients in the low-risk group were more sensitive to immunotherapy targeting PD-1 and CTLA-4.ConclusionOur study constructed a prognostic signature based on 10 AAMRGs, which could be used to build a novel prognosis model and identify potential drug candidates for the treatment of COAD.

Integration of Transcriptomics and Metabolomics Reveals the Antitumor Mechanism Underlying Tadalafil in Colorectal Cancer.

The potential role of tadalafil, a PDE5 inhibitor, in anticancer activity and prolonged survival has been proposed. However, the systematic effects of tadalafil in colorectal cancer were not fully understood. In this study, we assessed the anti-tumor activity of tadalafil in human colorectal cancer cells. A systematic perspective of the tadalafil-induced anti-tumor mechanism was provided by the integration of transcriptomics and metabolomics. We found that differentially expressed genes (DEGs) were mainly involved in microRNAs in cancer, purine metabolism, glycosphingolipid biosynthesis, arginine biosynthesis, and amino acid metabolism. Amino acid metabolism, especially alanine, aspartate, and glutamate metabolism was the most of the differentially accumulated metabolites (DAMs) through the analysis of metabolomics. The conjoint analysis of DEGs and DAMs presented that they were also mainly involved in alanine, aspartate, and glutamate metabolism. Amino acid metabolism-related genes, GPT, GGT5, and TAT, were significantly decreased after tadalafil treatment. In particular, the disturbance of alanine, aspartate, and glutamate metabolism may be the explanation for the major mechanism resulting from tadalafil anti-tumor activity.

Amino Acid Metabolism-Related lncRNA Signature Predicts the Prognosis of Breast Cancer.

Background and Purpose: Breast cancer (BRCA) is the most frequent female malignancy and is potentially life threatening. The amino acid metabolism (AAM) has been shown to be strongly associated with the development and progression of human malignancies. In turn, long noncoding RNAs (lncRNAs) exert an important influence on the regulation of metabolism. Therefore, we attempted to build an AAM-related lncRNA prognostic model for BRCA and illustrate its immune characteristics and molecular mechanism. Experimental Design: The RNA-seq data for BRCA from the TCGA-BRCA datasets were stochastically split into training and validation cohorts at a 3:1 ratio, to construct and validate the model, respectively. The amino acid metabolism-related genes were obtained from the Molecular Signature Database. A univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) regression, and a multivariate Cox analysis were applied to create a predictive risk signature. Subsequently, the immune and molecular characteristics and the benefits of chemotherapeutic drugs in the high-risk and low-risk subgroups were examined. Results: The prognostic model was developed based on the lncRNA group including LIPE-AS1, AC124067.4, LINC01655, AP005131.3, AC015802.3, USP30-AS1, SNHG26, and AL589765.4. Low-risk patients had a more favorable overall survival than did high-risk patients, in accordance with the results obtained for the validation cohort and the complete TCGA cohort. The elaborate results illustrated that a low-risk index was correlated with DNA-repair–associated pathways; a low TP53 and PIK3CA mutation rate; high infiltration of CD4+ T cells, CD8+ T cells, and M1 macrophages; active immunity; and less-aggressive phenotypes. In contrast, a high-risk index was correlated with cancer and metastasis-related pathways; a high PIK3CA and TP53 mutation rate; high infiltration of M0 macrophages, fibroblasts, and M2 macrophages; inhibition of the immune response; and more invasive phenotypes. Conclusion: In conclusion, we attempted to shed light on the importance of AAM-associated lncRNAs in BRCA. The prognostic model built here might be acknowledged as an indispensable reference for predicting the outcome of patients with BRCA and help identify immune and molecular characteristics.

Gut bacterial profile associated with healthy and diseased (AHPND) shrimp Penaeus vannamei

The effect of Vibrio parahaemolyticus IPNGS16 on the bacterial profile of the gut of Penaeus vannamei was assessed by 16S metagenomic analysis. The V3 hypervariable region of the bacterial 16S rDNA was amplified by PCR. Sequencing reads were generated using the 2×150 (300 cycles) for the base-read length chemistry of the Illumina MiniSeq platform. The web-based Shaman and MicrobiomeAnalyst platforms were used to analyze the sequences. The phyla Proteobacteria, Bacteroidetes, and the genera Vibrio, Ruegeria, Nautella, and Pseudoalteromonas were found among the most abundant taxonomic ranks in control, diseased, and healthy shrimp. Alpha and beta indices showed significant differences between shrimp survival in the control condition and dying shrimp (lower diversity). Metabolism (carbohydrate and amino acid metabolism-related genes and, to a lesser extent, energy, lipid, and cofactors and vitamin metabolism-related genes) of dying and surviving shrimp was affected by Vibrio infection. The top metabolic functions (cell cycle, glycine, serine, threonine, cysteine, methionine, purine, pyrimidine, pyruvate, and quorum sensing) in dying and surviving shrimp were affected by Vibrio, especially quorum sensing. The interaction network analysis showed fewer interactions in dying shrimp than control and surviving shrimp. Proteobacteria, Bacteroidetes, Vibrio, and Ruegeria predominated in all samples, and Vibrio changed bacterial diversity and metabolism in the intestine of P. vannamei. Ruegeria and Pseudoalteromonas showed negative interactions with Vibrio, suggesting their use as probiotics. This study sheds light on the Vibrio infection in the gut microbiota of shrimp.

Transcriptomics Coupled to Proteomics Reveals Novel Targets for the Protective Role of Spermine in Diabetic Cardiomyopathy.

Background Diabetic cardiomyopathy (DbCM) is the main complication and the cause of high mortality of diabetes. Exploring the transcriptomics and proteomics of DbCM is of great significance for understanding the biology of the disease and for guiding new therapeutic targets for the potential therapeutic effect of spermine (SPM). Methods and Results By using a mouse DbCM model, we analyzed the overall transcriptome and proteome of the myocardium, before/after treatment with SPM. The general state and cardiac structure and function changes of each group were also compared. Diabetes induced an increased blood glucose and serum triglyceride content, a decreased body weight, serum insulin level, and cardiac function-related indexes, accompanied by disrupted myocardial tissue morphology and ultrastructure damage. Using RNA sequencing (RNA-seq), we identified thousands of differentially expressed genes (DEGs) in DbCM with or without SPM treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the DEGs were significantly enriched in lipid metabolism and amino acid metabolism pathways. Specifically, quantitative real-time PCR (qRT-PCR) confirmed that SPM protected DbCM by reversing the expressions of lipid metabolism and amino acid metabolism-related genes, including Alox15, Gm13033, pla2g12a, Ptges, Pnpla2, and Acot1. To further reveal the pathogenesis of DbCM, we used proteome-based data-independent acquisition (DIA) and identified 139 differentially expressed proteins (DEPs) with 67 being upregulated and 72 being downregulated in DbCM. Venn intersection analysis showed 37 coexpressed genes and proteins in DbCM, including 29 upregulation and 8 downregulation in DbCM. In the protein-protein interaction (PPI) network constructed by the STRING database, the metabolism-related coexpressed genes and proteins, such as Acot2, Ephx2, Cyp1a1, Comt, Acox1, Hadhb, Hmgcs2, Acot1, Inmt, and Cat, can interact with the identified DEGs and DEPs. Conclusion The biomarkers and canonical pathways identified in this study may hold the key to understand the mechanisms of DbCM pathobiology and provide new targets for the therapeutic effect of SPM against DbCM by targeting lipid and amino acid metabolism pathways.

Aquaporins in Pacific White Shrimp (Litopenaeus vannamei): Molecular Characterization, Expression Patterns, and Transcriptome Analysis in Response to Salinity Stress

Aquaporins (AQPs) are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. These proteins are vital for maintaining water homeostasis in living organisms. In mammals, thirteen aquaporins have been characterized, but in crustaceans, especially penaeid shrimp, the diversity, structure, and substrate specificity of these membrane channel proteins are largely unknown. We here presented the three types of AQPs from Litopenaeus vannamei based on genome and transcriptome sequencing. Phylogenetic analysis showed that each AQP separately represented members of aquaglyceroporins, classical aquaporins, and unorthodox aquaporins, thus they were named as LvAQP3, LvAQP4, and LvAQP11. The LvAqp4 was mostly expressed in hepatopancreas, stomach, and gill, meanwhile LvAqp3 and LvAqp11 were separately predominantly expressed in intestine and muscle, respectively. To investigate possible roles of aquaporins in osmoregulation, mRNA expression changes in mainly expressed tissues were analyzed after acute exposure or long-term acclimation to different salinities. The results revealed that the expression levels of aquaporins genes were significantly decreased in most tissues (except hepatopancreas) under salinity stress, though the expression patterns were variable among isoforms and tissues. Moreover, comparative transcriptome analysis indicated the combination roles of aquaglyceroporin and amino acid metabolism related genes and pathways in response to acute salinity changes in the intestine. This study opened new windows for future investigations and provided new insights into the role of aquaporins in osmoregulation in L. vannamei.

Development and Clinical Validation of a Novel 10-Gene Signature Based on Amino Acid Metabolism-Related Genes in Colorectal Cancer

Development and Clinical Validation of a Novel 10-Gene Signature Based on Amino Acid Metabolism-Related Genes in Colorectal Cancer

Alterations of amino acid metabolism and intestinal microbiota in Chinese mitten crab (Eriocheir sinensis) fed on formulated diet and iced trash fish

Formulated diet (FD) and iced trash fish (ITF) are common diets during E. sinensis farming. However, whether FD can completely replace ITF during long-term E. sinensis farming is still unclear. Thus this study was conducted to compare the differences in amino acid metabolism and intestinal microbiota of the E. sinensis fed on different diets. The crabs were randomly divided into three groups fed on FD, ITF and mixed diet (MD, FD: ITF = 1:1), respectively. The results showed that there were no significant differences in amino acid composition among FD, MD and ITF groups. The activities of AST and ALT, and the mRNA levels of amino acid metabolism-related genes were significantly up-regulated in FD or/and MD groups compared with ITF group. The diversity of intestinal bacterial community was similar between the FD and ITF groups, but the relative abundance of dominant taxa showed marked differences between the two groups. At the phylum level, the relative abundance of Firmicutes was significantly higher, but the relative abundance of Proteobacteria was significantly lower in the FD group than that in ITF group. Meanwhile, at genus level, the relative abundance of Candidatus_Hepatoplasma in FD was higher than that in ITF group. Data related to functional prediction demonstrated that the significantly differenced pathways between the two groups were observed in metabolism (Pyrimidine metabolism, Glycolysis/Gluconeogenesis and Citrate cycle) and environmental information processing (transporters). The overall results indicated that replacement of ITF by FD did not affect amino acid composition, but altered amino acid metabolism and the relative abundance of intestinal microbiota. Our data provided a valuable reference for FD application replacing ITF during long-term E. sinensis farming.

OsDOF11 Affects Nitrogen Metabolism by Sucrose Transport Signaling in Rice (Oryza sativa L.).

Carbon and nitrogen antagonistically regulate multiple developmental processes. However, the molecular mechanism affecting nitrogen metabolism by sucrose transport remains poorly defined. Previously, we noted that Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11) mediated sucrose transport by binding to the promoter regions of Sucrose Transporter 1 (SUT1), Oryza sativa Sugars Will Eventually be Exported Transporters 11 (OsSWEET11), and OsSWEET14. Here, we note that OsDOF11 promotes nitrogen uptake and then maintains the ratio of fresh weight to dry weight in seedling plants and the effective leaf blade at flowering stages. Mutants of the sucrose transporter gene OsSWEET14 displayed a phenotype similar to that of OsDOF11. By microarray analysis and qRT-PCR in OsDOF11 mutant plants, OsDOF11 affected the transcription level of amino acid metabolism-related genes. We further found that mainly amino acid contents were reduced in flag leaves but increased in seeds. Both sugar and organic nitrogen changes caused the ratio of fresh weight to dry weight to decrease in OsDOF11 mutant seedling plants and mature leaves, which might result in vigorous reduced metabolic activity and become less susceptible to stress. These results demonstrated that OsDOF11 affected nitrogen metabolism by sugar distribution in rice, which provided new insight that OsDOF11 coordinated with C and N balance to maintain plant growth activity.

Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC.

Background: Hepatocellular carcinoma (HCC) is the world’s second most deadly cancer, and metabolic reprogramming is its distinguishing feature. Among metabolite profiling, variation in amino acid metabolism supports tumor proliferation and metastasis to the most extent, yet a systematic study on the role of amino acid metabolism-related genes in HCC is still lacking. An effective amino acid metabolism-related prediction signature is urgently needed to assess the prognosis of HCC patients for individualized treatment.Materials and Methods: RNA-seq data of HCC from the TCGA-LIHC and GSE14520 (GPL3921) datasets were defined as the training set and validation set, respectively. Amino acid metabolic genes were extracted from the Molecular Signature Database. Univariate Cox and LASSO regression analyses were performed to build a predictive risk signature. K-M curves, ROC curves, and univariate and multivariate Cox regression were conducted to evaluate the predictive value of this risk signature. Functional enrichment was analyzed by GSEA and CIBERSORTx software.Results: A nine-gene amino acid metabolism-related risk signature including B3GAT3, B4GALT2, CYB5R3, GNPDA1, GOT2, HEXB, HMGCS2, PLOD2, and SEPHS1 was constructed to predict the overall survival (OS) of HCC patients. Patients were separated into high-risk and low-risk groups based on risk scores and low-risk patients had lower risk scores and longer survival time. Univariate and multivariate Cox regression verified that this signature was an independent risk factor for HCC. ROC curves showed that this risk signature can effectively predict the 1-, 2-, 3- and 5-year survival times of patients with HCC. Additionally, prognostic nomograms were established based on the training set and validation set. These genes were closely correlated with the immune regulation.Conclusion: Our study identified a nine-gene amino acid metabolism-related risk signature and built predictive nomograms for OS in HCC. These findings will help us to personalize the treatment of liver cancer patients.

Axl-inhibitor bemcentinib alleviates mitochondrial dysfunction in the unilateral ureter obstruction murine model.

Renal fibrosis is a progressive histological manifestation leading to chronic kidney disease (CKD) and associated with mitochondrial dysfunction. In previous work, we showed that Bemcentinib, an Axl receptor tyrosine kinase inhibitor, reduced fibrosis development. In this study, to investigate its effects on mitochondrial dysfunction in renal fibrosis, we analysed genome‐wide transcriptomics data from a unilateral ureter obstruction (UUO) murine model in the presence or absence of bemcentinib (n = 6 per group) and SHAM‐operated (n = 4) mice. Kidney ligation resulted in dysregulation of mitochondria‐related pathways, with a significant reduction in the expression of oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), citric acid cycle (TCA), response to reactive oxygen species and amino acid metabolism‐related genes. Bemcentinib treatment increased the expression of these genes. In contrast, AKT/PI3K signalling pathway genes were up‐regulated upon UUO, but bemcentinib largely inhibited their expression. At the functional level, ligation reduced mitochondrial biomass, which was increased upon bemcentinib treatment. Serum metabolomics analysis also showed a normalizing amino acid profile in UUO, compared with SHAM‐operated mice following bemcentinib treatment. Our data suggest that mitochondria and mitochondria‐related pathways are dramatically affected by UUO surgery and treatment with Axl‐inhibitor bemcentinib partially reverses these effects.

Effect of dietary inulin in the gut microbiota of whiteleg shrimp Penaeus vannamei

The effect of dietary inulin on the intestinal bacterial communities of Penaeus vannamei by 16S metagenomic analysis was assessed. PCR amplified the V3 region of the bacterial 16S rDNA. Sequencing reads were generated using the 2×150 (300 cycles) for the base-read length chemistry of the Illumina MiniSeq platform. The software Shaman and MicrobiomeAnalyst were used to analyze the sequences. The phylum Proteobacteria and the genus Vibrio were among the most abundant taxonomic ranks for control and inulin treatment. The relative abundance of the phylum Bacteroidetes and genus Ruegeria was lower in inulin treatment concerning the control condition. Alpha and beta indices did not show significant differences between inulin treatment and control conditions. For all samples, most of the bacterial organisms showed the presence of carbohydrate and amino acid metabolism-related genes, and to a lesser extent, of energy, lipid, and cofactors and vitamin metabolism-related genes. The principal metabolic functions were glycine, serine, threonine, glyoxylate and dicarboxylate, purine, pyrimidine, pyruvate, and quorum sensing. The interaction network analysis showed fewer interactions in the inulin treatment concerning control condition. Proteobacteria, Bacteroidetes, Vibrio, and Ruegeria predominated in all samples, and inulin did not change the net microbial diversity in the intestine of P. vannamei. Streptomyces, Roseobacter, and Ruegeria showed negative interactions with Vibrio, suggesting their use as probiotics. This study sheds light on the inulin supplement on the essential role of microbiota in the shrimp.

Transcriptomic Responses Induced in Muscle and Adipose Tissues of Growing Pigs by Intravenous Infusion of Sodium Butyrate.

Simple SummaryThe present study was constructed to determine the effects of short-term intravenous sodium butyrate (SB) administration on metabolism through transcriptomic responses in muscle and adipose tissue of pigs. We found that systemic butyrate displayed a discriminative metabolic regulation in muscle and adipose tissue. Intravenous SB infusion decreased amino acid metabolism pathways both in muscle and adipose tissues. Intravenous SB infusion increased glucose catabolism in muscle tissue and decreased glucose utilization in adipose tissue. Moreover, intravenous SB infusion decreased lipolysis in muscle tissue but increased lipolysis in adipose tissue. These findings support the direct role of the SCFA butyrate in the regulation of the metabolism.Butyrate has a central function in the regulation of energy metabolism as a metabolite of bacterial fermentation. This study evaluated the effects of intravenous sodium butyrate (SB) administration on the transcriptome of muscle and adipose tissue of pigs. Twelve crossbred barrows (Duroc × Landrace × Large White) were fitted with a medical polyethylene cannula via the internal jugular vein and were daily infused with 10 mL SB (200 mmol/L) or the same volume of physiological saline. Muscle transcriptome showed 11 DEGs related to carbohydrate metabolism, 28 DEGs related to lipid metabolism, and 10 DEGs related to amino acid metabolism. Among these, carbohydrate catabolic process-related genes (PPP1R3B, PRPS2, ALDOC), fatty acid synthase (FASN), and lipolysis-related genes (PLIN1) were upregulated, while the carbohydrate biosynthetic process-related genes (PCK1) and most amino acid metabolism-related genes were downregulated. Adipose transcriptome showed 12 DEGs related to carbohydrate metabolism, 27 DEGs related to lipid metabolism, and 10 DEGs related to amino acid metabolism. Among these, carbohydrate metabolism-related genes (IGF1, LEP, SLC2A4) and lipolysis-related genes (LPL) were upregulated, while lipolysis-related genes (ANGPTL4) and most amino acid metabolism-related genes were downregulated. The results suggest that short-term intravenous SB infusion could modulate the muscle and adipose tissue metabolism at the transcriptional level by decreasing amino acid metabolism pathways. Additionally, intravenous SB increased the glucose catabolism in muscle tissue and decreased the glucose utilization in adipose tissue. Intravenous SB increased the fatty acid synthesis, decreased the lipolysis in muscle tissue, and increased the lipolysis in adipose tissue. This suggests that systemic butyrate may display discriminative metabolic regulation in different tissues of barrows.

Transcriptomic evidence of adaptive tolerance to high environmental ammonia in mudskippers

Mudskippers are typical amphibious fishes and possess various strategies to ameliorate ammonia toxicity during exposure to environmental ammonia. The present study aimed to provide transcriptomic evidence through profiling the gill and liver transcriptomes of Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM), which were subjected to treatment with high environmental ammonia for up to 72 h. The results of gene function annotation showed that most of the differentially expressed genes were involved in metabolic pathways. After ammonia exposure, the protein and amino acid metabolism related genes in mudskippers were down-regulated, and PM had more down-regulated genes than BP. The expression levels of several representative genes involved in ammonia excretion in the gill were commonly increased. Interestingly, NH4+ transporting and H+ excreting related genes, including Na+/K+(NH4+)/2Cl− cotransporter (nkcc), Na+/K+(NH4+)-ATPase (nka), carbonic anhydrase 2 (ca2), H+-ATPase, Na+/H+ (NH4+)-exchanger (nhe), and carbonic anhydrase 15 (ca15), were up-regulated more significantly in BP than PM; however, the transcription levels of Rhesus glucoprotein b (Rhbg) and Rhesus glucoprotein c1 (Rhcg1), which constitute the NH3 transporting channels, were up-regulated more significantly in PM than BP. Furthermore, the present study provides molecular evidence for how mudskippers adopt partial amino acid catabolism to decrease the production of endogenous ammonia under high environmental ammonia loading.

Disorder of gut amino acids metabolism during CKD progression is related with gut microbiota dysbiosis and metagenome change

Chronic kidney disease (CKD) is a worldwide public health problem. Uremic retention solutes such as indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are accumulated in CKD patients and are associated with the incidence of CKD progression. Amino acids are the major precursors of uremic retention solutes in gut. The dynamic change of amino acid metabolism in the gut during CKD progression has not been reported previously. In this paper, we studied the dynamic change of gut IS/PCS precursor and amino acid metabolism profile during CKD progression in 5/6 nephrectomized (5/6Nx) rats model. The related gut microbiota and metagenome profile was also studied. Rat plasma, urine and feces were collected at different time points after nephrectomization. Plasma IS and PCS, fecal indole (the precursor of IS), p-cresol (the precursor of PCS) and 19 kinds of amino acids were analyzed by LC–MS. During CKD progression, 5/6 Nx rats showed increased plasma IS, PCS concentration and increased fecal indole, p-cresol concentration. 5/6 Nx rats also showed disordered gut amino acids metabolism profile which became more significant along with the progession of CKD. The abundance of some specific gut bacteria also changed significantly in 5/6 Nx rats. The 16S rDNA sequencing data of gut microbiota was further analyzed by an online tool PICRUSt, a large-scale computational method for metagenomes prediction with 16S rDNA sequencing data. The content of each gene was compared between the two groups by Mann-Whitney U test, and then the significantly regulated genes in 5/6 Nx group were subjected to KEGG website. The amino acid metabolism related genes were picked out. Most of these genes are more abundant in 5/6 Nx groups. Our study showed that gut amino acids metabolism profile was disordered with CKD progression, which was highly related to the gut microbiota dysbiosis and metagenome change. And that regulation of gut amino acids metabolism pathway may be a possible way to intervene the progression of CKD.

Abstract 4197: Interaction of B lymphoma cells with the microenvironment affects ibrutinib sensitivity

Abstract Introduction: The cellular microenvironment plays a key role in the pathogenesis of B-cell malignancies (Amé-Thomas, Blood 2007; Podar, Leukemia 2009). Bone marrow stromal cell interactions can provide survival signals to CLL cells (Kurtova, Blood 2009), and stromal cell gene signatures and markers can predict survival outcomes and add prognostic value, respectively, for patients with DLBCL (Lenz, NEJM 2008; Meyer, Am J Clin Pathol 2011). Ibrutinib (ibr), a first-in-class, oral, once-daily inhibitor of Bruton’s tyrosine kinase, has demonstrated single-agent activity in R/R DLBCL (Wilson, Nat Med 2015). In this study, we established an in vitro coculture system and report the effects of stromal cells on ABC-DLBCL cells and their sensitivity to ibr. Methods: The effect of ibr on cell growth was evaluated by luminescent cell viability assay. Flow cytometry was used to evaluate the effect of ibr on cell death in different cell populations. Live-cell imaging detected drug effects on apoptosis at different time points. Gene expression levels in B lymphoma cells were examined by quantitative PCR and NanoString panels. Human cytokines/chemokines were quantified using MILLIPLEX® MAP Kit. Results: Reduced ibr sensitivity was observed in TMD8 DLBCL cells cocultured with HS-5 bone marrow-derived stromal cells. HS-5 cells protected TMD8 cells from ibr-induced apoptosis. Treatment with ibr induced TNFSF10 expression only in TMD8 cells without HS-5 coculture, providing a survival mechanism for escape of ibr-induced cell death. In addition, coculturing with HS-5 decreased surface expression of CD20 but not CD19. Several cytokines/chemokines showed differential expression in the coculture system (increased CCL22 and IL-10; decreased CCL4 and TNFβ). Reduced expression of BCR signaling-related miR-155 was observed in ABC-DLBCL and CLL cell lines with HS-5 coculture, suggesting downregulation of BCR signaling in these cells. The adhesion molecule, SELL, showed decreased expression in the ABC-DLBCL cells cultured with HS-5 as well as in ibr-resistant TMD8 cells, consistent with our observation that ABC-DLBCL patients with poor responses (PD+SD) to ibr have lower SELL expression in their tumor samples. We further assessed expression levels of amino acid metabolism-related genes and demonstrated significant increases of ASS1 and TDO2 in the TMD8 cells cocultured with HS-5. Expression levels of amino acid metabolism-related genes varied across patients with different responses to ibr, further suggesting the importance of amino acid levels in the tumor microenvironment and ibr response. Conclusions: The changes in ABC-DLBCL cells cocultured with stromal cells identified here may provide new insights into cellular cross-talk in the microenvironment. Further investigation into cell-cell interactions and ibr may help stratify patient populations and provide new therapeutic strategies. Citation Format: Hsu-Ping Kuo, Sidney Hsieh, Mint Sirisawad, Chun-Te Chen, Leo W. Cheung, Karl J. Schweighofer, Chia-Lin Hsu, Chi-Ling Fu, Jing Liu, Shiquan Wu, Karl Eckert, Hugh Wang, Mutiah Apatira, Kamaldeep Dhami, Kevin Kwei, Jeff Hsu, Betty Y. Chang. Interaction of B lymphoma cells with the microenvironment affects ibrutinib sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4197. doi:10.1158/1538-7445.AM2017-4197

Comparison of amino acid profiles and metabolic gene expression in muskrat scented glands in secretion and non-secretion season

The scented gland is an organ responsible for producing musk in muskrats. During musk secretion season, the metabolism of glandular cells increases in the scented glands and a large amount of musk is synthesised. In this study, we collected scented gland arterial blood from six healthy adult male muskrats during non-secretion season (November). We also obtained scented gland arterial blood, venous blood, and musk from six healthy adult males during secretion season (March). Qualitative and quantitative analyses of free amino acids in blood and musk were performed with an automated amino acid analyzer. Additionally, we employed RNA sequencing technology to study the expression patterns of amino acid metabolic pathways in scented glands. Amino acid profile analysis indicates that scented glands can concentrate amino acids during secretion season, and transcriptome analysis suggests that some amino acid metabolism-related genes undergo significant seasonal changes. In summary, scented gland amino acid metabolism displays seasonal differences. Elevated amino acid metabolic activity during secretion season sustains the glands’ secretory function.

Transcriptional changes in oysters Crassostrea brasiliana exposed to phenanthrene at different salinities

Euryhaline animals from estuaries, such as the oyster Crassostrea brasiliana, show physiological mechanisms of adaptation to tolerate salinity changes. These ecosystems receive constant input of xenobiotics from urban areas, including polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene (PHE). In order to understand the influence of salinity on the molecular responses of C. brasiliana exposed to PHE, oysters were acclimatized to different salinities (35, 25 and 10) for 15days and then exposed to 100μgL−1 PHE for 24h and 96h. Control groups were kept at the same salinities without PHE. Oysters were sampled for chemical analysis and the gills were excised for mRNA quantification by qPCR. Transcript levels of different genes were measured, including some involved in oxidative stress pathways, phases I and II of the xenobiotic biotransformation systems, amino acid metabolism, fatty acid metabolism and aryl hydrocarbon receptor nuclear translocator putative gene. Higher transcript levels of Sulfotransferase-like gene (SULT-like) were observed in oysters exposed to PHE at salinity 10 compared to control (24h and 96h); cytochrome P450 isoforms (CYP2AU1, CYP2-like1) were more elevated in oysters exposed for 24h and CYP2-like2 after 96h of oysters exposed to PHE at salinity 10 compared to control. These results are probably associated to an enhanced Phase I biotransformation activity required for PHE detoxification under hyposmotic stress. Higher transcript levels of CAT-like, SOD-like, GSTm-like (96h) and GSTΩ-like (24h) in oysters kept at salinity 10 compared to organisms at salinities 25 and/or 35 are possibly related to enhaced ROS production. The transcription of these genes were not affected by PHE exposure. Amino acid metabolism-related genes (GAD-like (24h), GLYT-like, ARG-like (96h) and TAUT-like at 24h and 96h) also showed different transcription levels among organisms exposed to different salinities, suggesting their important role for oyster salinity adaptation, which is not affected by exposure to these levels of PHE.

Imprinted gene OsFIE1 modulates rice seed development by influencing nutrient metabolism and modifying genome H3K27me3.

Imprinted Polycomb group (PcG) genes play a critical role in seed development in Arabidopsis. However, the role of the imprinted gene in cereal plants remains obscure. Here, a transgenic approach was conducted to study the function of the imprinted gene Oryza sativa Fertilization-Independent Endosperm 1 (OsFIE1) during seed development in rice (Oryza sativa ssp. japonica 'ZhongHua11'). RNAi of OsFIE1 and homozygous T-DNA insertion mutant osfie1 led to smaller seeds, delayed embryo development, smaller aleurone layer cells, and decreased seed set rate. OsFIE1 was specifically expressed in endosperm, and mRNA of OsFIE1 was also enriched in the inner seed coat together with the corresponding PcG members OsiEZ1 and OsCLF. Meanwhile, the contents of seed storage proteins and Ile, Leu, and Val were decreased, accompanied by the down-regulation of multiple transcription factors, storage protein synthesis and amino acid metabolism-related genes in OsFIE1-RNAi lines and osfie1. Western blot analysis showed that the complex OsFIE1-PcG in endosperm regulated the expression of target genes by genome H3K27me3 modification. We conclude that the OsFIE1-PcG complex, which was enriched in the inner seed coat and endosperm linked the development of embryo and endosperm by influencing transcription factors and nutrient metabolism and induced a highly differential effect when compared with the OsFIE2-PcG complex.