scholarly journals Ring sideroblasts in AML are associated with adverse risk characteristics and have a distinct gene expression pattern

2019 ◽  
Vol 3 (20) ◽  
pp. 3111-3122
Author(s):  
Gerbrig Berger ◽  
Mylene Gerritsen ◽  
Guoqiang Yi ◽  
Theresia N. Koorenhof-Scheele ◽  
Leonie I. Kroeze ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Gene Expression Pattern ◽  
Erythroid Differentiation ◽  
Tp53 Mutations ◽  
Expression Studies ◽  
Risk Characteristics ◽  
Key Points ◽  
Ring Sideroblasts ◽  
Gene Expression Studies

Key Points Ring sideroblasts in AML are associated with complex karyotypes and TP53 mutations. Gene expression studies in CD34+ AML cells suggest an altered erythroid differentiation program in AML with ring sideroblasts.

scholarly journals A Scientific Note of Housekeeping Genes for the Primitively Eusocial bee Euglossa viridissima Friese (Apidae: Euglossini)

Sociobiology ◽  
2018 ◽  
Vol 65 (4) ◽  
pp. 766
Author(s):  
Samuel Boff ◽  
Anna Friedel ◽  
Anja Miertsch ◽  
J. Javier Quezada-Euàn ◽  
Robert J Paxton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Reference Genes ◽  
Developmental Stages ◽  
Gene Expression Pattern ◽  
Housekeeping Genes ◽  
Expression Of Genes ◽  
Gene Expression Studies ◽  
The Stability ◽  
Primitively Eusocial

Studies on the expression of genes in different contexts are essential to our understanding of the functioning of organisms and their adaptations to the environment. Gene expression studies require steps of normalization, which are done using the stable expression pattern of reference genes. For many different eusocial bees reference genes have been discovered, but not for the primitively eusocial euglossine bees.We used available genomic resources of euglossine species and the gene information of Apis melliferato develop a set of reference genes for the primitive eusocial bee Euglossaviridissima. We tested nine genes in distinct developmental stages three different algorithms to infer the stability of gene expression. The Tata binding protein(Tbp) and 14-3-3epsilon were the most stable genes across all different stages. The strongest deviation in gene expression pattern occurred in pupae, which require a different set of genes for normalizing gene expression. 

A nine-gene predictor of therapy response in adult Philadelphia-chromosome positive acute lymphoblastic leukemia (Ph+ ALL)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 7014-7014
Author(s):  
Z. Zuo ◽  
D. M. Jones ◽  
D. A. Thomas ◽  
S. O'Brien ◽  
F. Ravandi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Gene Expression Pattern ◽  
Therapy Response ◽  
Response To Therapy ◽  
Support Vector ◽  
Published Data ◽  
Expression Studies ◽  
Gene Predictor ◽  
Response Expression

7014 Background: Ph+ ALL in adults shows a poor response to therapy and high frequency of relapse. This study utilized a meta-analysis of previous genome-wide gene expression studies to define and validate a nine-gene predictor of outcome in Ph+ ALL patients. Methods: Normalized gene expression data from previously published studies of 672 ALL patients were analyzed to identify genes associated with therapy response. Expression of the selected genes was assessed using Applied Biosystems low density reverse transcription quantitative PCR (RT-qPCR) arrays in bone marrow (BM) samples from 27 adult Ph+ ALL patients treated with standard chemotherapy plus a tyrosine kinase inhibitor. Therapy responses were defined at the molecular level by monitoring BCR/ABL1 levels, and categorized into 3 groups: optimal, persistent and relapse. Median follow up was 6 months (range 4–15). Median disease-free survival among the optimal and relapse groups were 12 and 5 months respectively (p = 0.002). There was no statistical difference in age, initial peripheral blood white cell and BM blast counts, and initial normalized BCR/ABL1 levels between groups. Differentially expressed genes were selected using the significance analysis of microarrays (SAM). Hierarchical clustering and principal component analysis were applied to assess the correlation between gene expression pattern and therapy response. A predictive model was built using support vector machines. Differences in survival among groups were compared by Kaplan-Meier analysis. Results: Data mining and pathway analysis of the published data identified 46 genes in 7 pathways potentially associated with therapy response (p < 0.001). RT-qPCR results from a 15 case training set, 5 in each outcome group, identified 9 genes that classified the cases with 100% accuracy. Validation using an additional 12 cases showed 91.7% prediction accuracy (ROC error = 0.056). Compared with the initial diagnostic samples, gene expression pattern in relapsed samples shifted to that resembling the persistent group. Conclusions: Using data-trimming of whole genome expression studies, we defined and validated a nine-gene signature that is an independent predictive marker for therapy response in adult Ph+ ALL patients. No significant financial relationships to disclose.

Gene expression pattern of chicken erythrocyte nuclei in heterokaryons

1990 ◽  
Vol 97 (1) ◽  
pp. 167-175
Author(s):  
M. Bergman ◽  
N. Ringertz
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Globin Gene ◽  
Gene Expression Pattern ◽  
Erythroid Differentiation ◽  
Specific Gene ◽  
Globin Genes ◽  
Beta Globin ◽  
Beta Globin Gene ◽  
Strong Expression

Expression of erythro-specific chick genes was studied in heterokaryons prepared by fusing chick erythrocytes (CE) with rat myoblasts. In this type of heterokaryon the inactive erythrocyte nucleus takes up nuclear proteins of myoblast origin and undergoes transcriptional reactivation. In order to study the stability of the genetic programming of the reactivated CE nucleus, chick gene expression was examined by analysis of RNA from the heterokaryons. Probes for several erythro- and chick-specific genes were used. The heterokaryons showed strong expression of the chick histone H5 and adult alpha-globin genes, while other genes, e.g. the transcription factor Eryf1 gene, normally expressed during erythroid differentiation, were not transcribed. Although the CE used were of the definitive lineage, the heterokaryons showed activation of the chick embryonic beta-globin gene, i.e. a gene normally expressed only in CE of the primitive lineage. We conclude that the reactivation of the mature CE nucleus in a rat cytoplasm resulted in a more immature erythroid gene expression pattern. The activation of the embryonic beta-globin gene indicated a switch of the lineage-specific gene expression pattern. This switch occurred in the absence of DNA replication. The strong expression of the globin and H5 genes in heterokaryons, in the absence of expression of the regulatory factor Eryf1, suggested the existence of Eryf1-independent regulatory mechanisms for erythroid gene expression in these cells.

scholarly journals Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kim Hoa Ho ◽  
Annarita Patrizi
Keyword(s):  
Gene Expression ◽  
Choroid Plexus ◽  
Sensory Deprivation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Experimental Conditions ◽  
Brain Repair ◽  
Expression Studies ◽  
Testing Algorithms ◽  
Gene Expression Studies

AbstractChoroid plexus (ChP), a vascularized secretory epithelium located in all brain ventricles, plays critical roles in development, homeostasis and brain repair. Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular and useful technique for measuring gene expression changes and also widely used in ChP studies. However, the reliability of RT-qPCR data is strongly dependent on the choice of reference genes, which are supposed to be stable across all samples. In this study, we validated the expression of 12 well established housekeeping genes in ChP in 2 independent experimental paradigms by using popular stability testing algorithms: BestKeeper, DeltaCq, geNorm and NormFinder. Rer1 and Rpl13a were identified as the most stable genes throughout mouse ChP development, while Hprt1 and Rpl27 were the most stable genes across conditions in a mouse sensory deprivation experiment. In addition, Rpl13a, Rpl27 and Tbp were mutually among the top five most stable genes in both experiments. Normalisation of Ttr and Otx2 expression levels using different housekeeping gene combinations demonstrated the profound effect of reference gene choice on target gene expression. Our study emphasized the importance of validating and selecting stable housekeeping genes under specific experimental conditions.

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