scholarly journals Cytokinin levels and expression profiles of cytokinin metabolic genes in late stage maize kernels

2018 ◽  
Vol 10 (4) ◽  
pp. 28-75
Author(s):  
Li Hong ◽  
M. G. Duff Stephen ◽  
Bedair Mohamed ◽  
Fernandes Mary ◽  
R. Dietrich Chuck
Keyword(s):  
Late Stage ◽  
Expression Profiles ◽  
Metabolic Genes ◽  
Maize Kernels

scholarly journals Early and late stage MPN patients show distinct gene expression profiles in CD34+ cells

2021 ◽  
Author(s):  
Julian Baumeister ◽  
Tiago Maié ◽  
Nicolas Chatain ◽  
Lin Gan ◽  
Barbora Weinbergerova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Late Stage ◽  
Rna Splicing ◽  
Bone Marrow Cells ◽  
Myeloproliferative Neoplasms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Primary Myelofibrosis ◽  
Estrogen Signaling ◽  
Therapeutic Modalities

AbstractMyeloproliferative neoplasms (MPN), comprising essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF), are hematological disorders of the myeloid lineage characterized by hyperproliferation of mature blood cells. The prediction of the clinical course and progression remains difficult and new therapeutic modalities are required. We conducted a CD34+ gene expression study to identify signatures and potential biomarkers in the different MPN subtypes with the aim to improve treatment and prevent the transformation from the rather benign chronic state to a more malignant aggressive state. We report here on a systematic gene expression analysis (GEA) of CD34+ peripheral blood or bone marrow cells derived from 30 patients with MPN including all subtypes (ET (n = 6), PV (n = 11), PMF (n = 9), secondary MF (SMF; post-ET-/post-PV-MF; n = 4)) and six healthy donors. GEA revealed a variety of differentially regulated genes in the different MPN subtypes vs. controls, with a higher number in PMF/SMF (200/272 genes) than in ET/PV (132/121). PROGENγ analysis revealed significant induction of TNFα/NF-κB signaling (particularly in SMF) and reduction of estrogen signaling (PMF and SMF). Consistently, inflammatory GO terms were enriched in PMF/SMF, whereas RNA splicing–associated biological processes were downregulated in PMF. Differentially regulated genes that might be utilized as diagnostic/prognostic markers were identified, such as AREG, CYBB, DNTT, TIMD4, VCAM1, and S100 family members (S100A4/8/9/10/12). Additionally, 98 genes (including CLEC1B, CMTM5, CXCL8, DACH1, and RADX) were deregulated solely in SMF and may be used to predict progression from early to late stage MPN. Graphical abstract

scholarly journals Construction and Validation of a Metabolic Reprogramming Related Prognostic Model for Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Xiaohong - Liu ◽  
Qian - Xu ◽  
Zi-Jing - Li ◽  
Bin - Xiong
Keyword(s):  
Hepatocellular Carcinoma ◽  
Regression Analysis ◽  
Risk Score ◽  
Prognostic Model ◽  
Cox Regression ◽  
Expression Profiles ◽  
Prognostic Significance ◽  
Metabolic Reprogramming ◽  
Cox Regression Analysis ◽  
Metabolic Genes

Abstract BackgroundMetabolic reprogramming is an important hallmark in the development of malignancies. Numerous metabolic genes have been demonstrated to participate in the progression of hepatocellular carcinoma (HCC). However, the prognostic significance of the metabolic genes in HCC remains elusive. MethodsWe downloaded the gene expression profiles and clinical information from the GEO, TCGA and ICGC databases. The differently expressed metabolic genes were identified by using Limma R package. Univariate Cox regression analysis and LASSO (Least absolute shrinkage and selection operator) Cox regression analysis were utilized to uncover the prognostic significance of metabolic genes. A metabolism-related prognostic model was constructed in TCGA cohort and validated in ICGC cohort. Furthermore, we constructed a nomogram to improve the accuracy of the prognostic model by using the multivariate Cox regression analysis.ResultsThe high-risk score predicted poor prognosis for HCC patients in the TCGA cohort, as confirmed in the ICGC cohort (P < 0.001). And in the multivariate Cox regression analysis, we observed that risk score could act as an independent prognostic factor for the TCGA cohort (HR (hazard ratio) 3.635, 95% CI (confidence interval)2.382-5.549) and the ICGC cohort (HR1.905, 95%CI 1.328-2.731). In addition, we constructed a nomogram for clinical use, which suggested a better prognostic model than risk score.ConclusionsOur study identified several metabolic genes with important prognostic value for HCC. These metabolic genes can influence the progression of HCC by regulating tumor biology and can also provide metabolic targets for the precise treatment of HCC.

scholarly journals CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants

2015 ◽  
Vol 197 (19) ◽  
pp. 3191-3205 ◽  
Author(s):  
Yun-Juan Bao ◽  
Zhong Liang ◽  
Jeffrey A. Mayfield ◽  
Shaun W. Lee ◽  
Victoria A. Ploplis ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Broad Spectrum ◽  
Virulence Genes ◽  
Expression Profiles ◽  
Altered Expression ◽  
Content Type ◽  
Metabolic Genes ◽  
A Genome ◽  
Group A ◽  
Regulated Gene Expression

ABSTRACTThe two-componentcontrolofvirulence (Cov) regulator (R)-sensor (S) (CovRS) regulates the virulence ofStreptococcus pyogenes(group AStreptococcus[GAS]). Inactivation of CovS during infection switches the pathogenicity of GAS to a more invasive form by regulating transcription of diverse virulence genes via CovR. However, the manner in which CovRS controls virulence through expression of extended gene families has not been fully determined. In the current study, the CovS-regulated gene expression profiles of a hypervirulentemm23GAS strain (M23ND/CovS negative [M23ND/CovS−]) and a noninvasive isogenic strain (M23ND/CovS+), under different growth conditions, were investigated. RNA sequencing identified altered expression of ∼349 genes (18% of the chromosome). The data demonstrated that M23ND/CovS−achieved hypervirulence by allowing enhanced expression of genes responsible for antiphagocytosis (e.g.,hasABC), by abrogating expression of toxin genes (e.g.,speB), and by compromising gene products with dispensable functions (e.g.,sfb1). Among these genes, several (e.g.,parEandparC) were not previously reported to be regulated by CovRS. Furthermore, the study revealed that CovS also modulated the expression of a broad spectrum of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination, where the bacteria encounter large variations in available nutrients, thus restructuring metabolism of GAS for adaption to diverse growth environments. From constructing a genome-scale metabolic model, we identified 16 nonredundant metabolic gene modules that constitute unique nutrient sources. These genes were proposed to be essential for pathogen growth and are likely associated with GAS virulence. The genome-wide prediction of genes associated with virulence identifies new candidate genes that potentially contribute to GAS virulence.IMPORTANCEThe CovRS system modulates transcription of ∼18% of the genes in theStreptococcus pyogenesgenome. Mutations that inactivate CovR or CovS enhance the virulence of this bacterium. We determined complete transcriptomes of a naturally CovS-inactivated invasive deep tissue isolate of anemm23strain ofS. pyogenes(M23ND) and its complemented avirulent variant (CovS+). We identified diverse virulence genes whose altered expression revealed a genetic switching of a nonvirulent form of M23ND to a highly virulent strain. Furthermore, we also systematically uncovered for the first time the comparative levels of expression of a broad spectrum of metabolic genes, which reflected different metabolic needs of the bacterium as it invaded deeper tissue of the human host.

scholarly journals Metabolic genes show excellent prognostic ability for clear cell renal cell carcinoma

2020 ◽  
Author(s):  
Chengjian Ji ◽  
Yichun Wang ◽  
Liangyu Yao ◽  
Jiaochen Luan ◽  
Rong Cong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Regression Analysis ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Cox Regression ◽  
Expression Profiles ◽  
Cell Renal Cell Carcinoma ◽  
Cox Regression Analysis ◽  
Metabolic Genes

Abstract Background Renal cell carcinoma (RCC) is one of the major malignant tumors of the urinary system, with a high mortality rate and a poor prognosis. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of RCC. Although the diagnosis and treatment methods have been significantly improved, the incidence and mortality of ccRCC are high and still increasing. The occurrence and development of ccRCC are closely related to the changes of classic metabolic pathways. This article aims to explore the relationship between metabolic genes and the prognosis of patients with ccRCC. Patients and methods: Gene expression profiles of 63 normal kidney tissues and 446 ccRCC tissues from TCGA database and gene expression profiles of 39 ccRCC tissues from GEO database were used to obtain differentially expressed genes (DEGs) in ccRCC. Through the the KEGG gene sets of GSEA database, we obtained metabolic genes (MGs). Univariate Cox regression analysis was used to identify prognostic MGs. Lasso regression analysis was used to eliminate false positives because of over-fitting. Multivariate Cox regression analysis was used to established a prognostic model. Gene expression data and related survival data of 101 ccRCC patients from ArrayExpress database were used for external validation. Survival analysis, ROC curve analysis, independent prognostic analysis and clinical correlation analysis were performed to evaluate this model. Results We found that there were 479 abnormally expressed MGs in ccRCC tissues. Through univariate Cox regression analysis, Lasso regression analysis and multivariate Cox regression analysis, we identified 4 prognostic MGs (P4HA3, ETNK2, PAFAH2 and ALAD) and established a prognostic model (riskScore). Whether in the training cohort, the testing cohort or the entire cohort, this model could accurately stratify patients with different survival outcomes. The prognostic value of riskScore and 4 MGs was also confirmed in the ArrayExpress database. Results of GSEA analysis show that DEGs in patients with better prognosis were enriched in metabolic pathways. Then, a new Nomogram with higher prognostic value was constructed to better predict the 1-year OS, 3-year OS and 5-year OS of ccRCC patients. In addition, we successfully established a ceRNA network to further explain the differences in the expression of these MGs between high-risk patients and low-risk patients Conclusion We have successfully established a risk model (riskScore) based on 4 MGs, which could accurately predict the prognosis of patients with ccRCC. Our research may shed new light on ccRCC patients' prognosis and treatment management.

Gene and Mirna Regulatory Networks During Different Stages of Crohn’s Disease

2019 ◽  
Vol 13 (7) ◽  
pp. 916-930 ◽  
Author(s):  
Sare Verstockt ◽  
Gert De Hertogh ◽  
Jan Van der Goten ◽  
Bram Verstockt ◽  
Maaike Vancamelbeke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Late Stage ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Cholesterol Biosynthesis ◽  
Newly Diagnosed ◽  
Relative Contribution ◽  
Regulatory Rnas

Abstract Background and Aims Early treatment of Crohn’s disease [CD] is required in order to optimize patient outcomes. To this end, we need to gain a better understanding of the molecular changes at the onset of CD. Methods As a model for the earliest mucosal CD lesions, we study post-operative recurrent CD [Rutgeerts score ≥ i2b]. We are the first to analyse gene and microRNA [miRNA] expression profiles in ileal biopsies from these patients, and compare them with those of newly diagnosed [≤18 months] and late-stage [>10 years after diagnosis] CD patients. Results Except for one gene [WNT5A], there are no differential genes in CD patients without post-operative recurrence [i0], showing that previous disease did not influence gene expression in the neoterminal ileum, and that this model can be used to study early mucosal CD lesions. Gene expression and co-expression network dysregulation is more pronounced in newly diagnosed and late-stage CD than in post-operative recurrent CD, with most important modules associated with [a]granulocyte adhesion/diapedesis, and cholesterol biosynthesis. In contrast, we found a role for snoRNAs/miRNAs in recurrent CD, highlighting the potential importance of regulatory RNAs in early disease stages. Immunohistochemistry confirmed the expression of key dysregulated genes in damaged/regenerating epithelium and immune cells in recurrent CD. Conclusions Aside from regulatory RNAs, there are no clear gene signatures separating post-operative recurrent, newly diagnosed, and late-stage CD. The relative contribution of dysregulated genes and networks differs, and suggests that surgery may reset the disease at the mucosal site, and therefore post-operative recurrent CD might be a good model a good model to study to study early mucosal CD lesions.

Bis deficiency results in early lethality with metabolic deterioration and involution of spleen and thymus

2008 ◽  
Vol 295 (6) ◽  
pp. E1349-E1357 ◽  
Author(s):  
Dong-Ye Youn ◽  
Dong-Hyoung Lee ◽  
Mi-Hyun Lim ◽  
Jung-Sook Yoon ◽  
Ji Hee Lim ◽  
...  
Keyword(s):  
Expression Profiles ◽  
White Blood Cells ◽  
Relative Weight ◽  
Postnatal Growth ◽  
Growth And Survival ◽  
Cholesterol Levels ◽  
Metabolic Genes ◽  
Cell Death Suppressor ◽  
Deficient Mice

Bcl-2 interacting cell death suppressor (Bis), also known as Bag3 or CAIR-1, is involved in antistress and antiapoptotic pathways. In addition to Bcl-2, Bis binds to several proteins, suggesting it has diverse functions in normal and pathological conditions. To better define the physiological function of Bis in vivo, we developed bis-deficient mice with a cre-loxP system. Targeted disruption of exon 4 of the bis gene was demonstrated by Southern blotting and PCR, and Western blotting showed that no intact or truncated Bis protein was synthesized in bis−/− mice. While heterozygotes were fertile and appeared normal, Bis-deficient mice showed growth retardation and died by 3 wk after birth. The relative weight of the thymus and spleen was reduced and the total numbers of white blood cells, splenocytes, and thymocytes were significantly reduced compared with wild-type littermates. Serum profiles indicated significant hypoglycemia as well as decrease in triglyceride and cholesterol levels. Expression profiles of metabolic genes indicated that gluconeogenesis and β-oxidation are activated in the liver of bis−/− mice. This activation, as well as a decrease in peripheral fat and an induction of fatty liver, appears to be an adaptive response to hypoglycemia. Our study reveals that the absence of Bis has considerable influences on postnatal growth and survival, possibly due to a nutritional impairment.

scholarly journals Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria

2016 ◽  
Vol 113 (52) ◽  
pp. 15102-15107 ◽  
Author(s):  
Olga A. Lastovetsky ◽  
Maria L. Gaspar ◽  
Stephen J. Mondo ◽  
Kurt M. LaButti ◽  
Laura Sandor ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Lipid Profile ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Metabolic Changes ◽  
Evolutionary Time ◽  
Rhizopus Microsporus ◽  
Mutualistic Symbiosis ◽  
Metabolic Genes ◽  
Bacterial Interaction

The recent accumulation of newly discovered fungal–bacterial mutualisms challenges the paradigm that fungi and bacteria are natural antagonists. To understand the mechanisms that govern the establishment and maintenance over evolutionary time of mutualisms between fungi and bacteria, we studied a symbiosis of the fungus Rhizopus microsporus (Mucoromycotina) and its Burkholderia endobacteria. We found that nonhost R. microsporus, as well as other mucoralean fungi, interact antagonistically with endobacteria derived from the host and are not invaded by them. Comparison of gene expression profiles of host and nonhost fungi during interaction with endobacteria revealed dramatic changes in expression of lipid metabolic genes in the host. Analysis of the host lipidome confirmed that symbiosis establishment was accompanied by specific changes in the fungal lipid profile. Diacylglycerol kinase (DGK) activity was important for these lipid metabolic changes, as its inhibition altered the fungal lipid profile and caused a shift in the host–bacterial interaction into an antagonism. We conclude that adjustments in host lipid metabolism during symbiosis establishment, mediated by DGKs, are required for the mutualistic outcome of the Rhizopus–Burkholderia symbiosis. In addition, the neutral and phospholipid profiles of R. microsporus provide important insights into lipid metabolism in an understudied group of oleaginous Mucoromycotina. Lastly, our study revealed that the DGKs involved in the symbiosis form a previously uncharacterized clade of DGK domain proteins.

scholarly journals Elevated seawater Pco2 differentially affects branchial acid-base transporters over the course of development in the cephalopod Sepia officinalis

2011 ◽  
Vol 300 (5) ◽  
pp. R1100-R1114 ◽  
Author(s):  
Marian Y. Hu ◽  
Yung-Che Tseng ◽  
Meike Stumpp ◽  
Magdalena A. Gutowska ◽  
Rainer Kiko ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Late Stage ◽  
Time Course ◽  
Expression Patterns ◽  
Somatic Growth ◽  
Sepia Officinalis ◽  
Ph Homeostasis ◽  
Metabolic Genes ◽  
Induced Changes

The specific transporters involved in maintenance of blood pH homeostasis in cephalopod molluscs have not been identified to date. Using in situ hybridization and immunohistochemical methods, we demonstrate that Na+/K+-ATPase ( soNKA), a V-type H+-ATPase ( soV-HA), and Na+/HCO3− cotransporter ( soNBC) are colocalized in NKA-rich cells in the gills of Sepia officinalis. mRNA expression patterns of these transporters and selected metabolic genes were examined in response to moderately elevated seawater Pco2 (0.16 and 0.35 kPa) over a time course of 6 wk in different ontogenetic stages. The applied CO2 concentrations are relevant for ocean acidification scenarios projected for the coming decades. We determined strong expression changes in late-stage embryos and hatchlings, with one to three log2-fold reductions in soNKA, soNBCe, socCAII, and COX. In contrast, no hypercapnia-induced changes in mRNA expression were observed in juveniles during both short- and long-term exposure. However, a transiently increased ion regulatory demand was evident during the initial acclimation reaction to elevated seawater Pco2. Gill Na+/K+-ATPase activity and protein concentration were increased by ∼15% during short (2–11 days) but not long-term (42-days) exposure. Our findings support the hypothesis that the energy budget of adult cephalopods is not significantly compromised during long-term exposure to moderate environmental hypercapnia. However, the downregulation of ion regulatory and metabolic genes in late-stage embryos, taken together with a significant reduction in somatic growth, indicates that cephalopod early life stages are challenged by elevated seawater Pco2.

scholarly journals Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancer

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Dagui Lin ◽  
Wenhua Fan ◽  
Rongxin Zhang ◽  
Enen Zhao ◽  
Pansong Li ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clustering Algorithm ◽  
Cox Regression ◽  
Molecular Subtype ◽  
Expression Profiles ◽  
Gene Expression Signature ◽  
Survival Prediction ◽  
Cox Regression Analysis ◽  
Metabolic Genes ◽  
Cluster A

Abstract Background Metabolic reprograming have been associated with cancer occurrence and progression within the tumor immune microenvironment. However, the prognostic potential of metabolism-related genes in colorectal cancer (CRC) has not been comprehensively studied. Here, we investigated metabolic transcript-related CRC subtypes and relevant immune landscapes, and developed a metabolic risk score (MRS) for survival prediction. Methods Metabolism-related genes were collected from the Molecular Signatures Database and metabolic subtypes were identified using an unsupervised clustering algorithm based on the expression profiles of survival-related metabolic genes in GSE39582. The ssGSEA and ESTIMATE methods were applied to estimate the immune infiltration among subtypes. The MRS model was developed using LASSO Cox regression in the GSE39582 dataset and independently validated in the TCGA CRC and GSE17537 datasets. Results We identified two metabolism-related subtypes (cluster-A and cluster-B) of CRC based on the expression profiles of 539 survival-related metabolic genes with distinct immune profiles and notably different prognoses. The cluster-B subtype had a shorter OS and RFS than the cluster-A subtype. Eighteen metabolism-related genes that were mostly involved in lipid metabolism pathways were used to build the MRS in GSE39582. Patients with higher MRS had worse prognosis than those with lower MRS (HR 3.45, P < 0.001). The prognostic role of MRS was validated in the TCGA CRC (HR 2.12, P = 0.00017) and GSE17537 datasets (HR 2.67, P = 0.039). Time-dependent receiver operating characteristic curve and stratified analyses revealed the robust predictive ability of the MRS in each dataset. Multivariate Cox regression analysis indicted that the MRS could predict OS independent of TNM stage and age. Conclusions Our study provides novel insight into metabolic heterogeneity and its relationship with immune landscape in CRC. The MRS was identified as a robust prognostic marker and may facilitate individualized therapy for CRC patients.

scholarly journals Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

2020 ◽  
Author(s):  
Kristopher Kieft ◽  
Zhichao Zhou ◽  
Rika Anderson ◽  
Alison Buchan ◽  
Barbara Campbell ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Niche Differentiation ◽  
Host Cells ◽  
Freshwater Lakes ◽  
Inorganic Sulfur ◽  
Metabolic Genes ◽  
Fitness Benefits ◽  
Auxiliary Metabolic Genes ◽  
Hydrothermal Environments

Abstract Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

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