Articles selected by Faculty of 1000: similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution

Abstract Introduction Cancer emerges as a consequence of multiple genetic aberrations that ultimately cause global changes in gene expression driving the malignant phenotype. Hence, identification of aberrantly expressed genes in cancer cells, as compared to their corresponding normal cells, provides information on the biology of the cancer as well as potential targets for therapeutic interventions. Here, we report an access-free internet platform for visualization of mRNA expression profiles in acute myeloid leukemia (AML) patient samples as compared to normal bone marrow (BM) populations representing successive stages of differentiation along the myeloid differentiation pathway. The internet platform allows for quick visualization of user selected genes in AML patients in either human or murine hematopoietic stem cells (HSC), myeloid hematopoietic progenitor cells (HPC) and their progeny, as well as mature cells of innate and adaptive immune system. Significantly, users can upload own microarray data to compare gene expression in their samples of interest to those available at the internet platform. Overall, our internet platform represents a powerful tool for studies of normal hematopoietic development as well as aberrantly expressed genes in AML and potentially other hematological malignancies. The web tool will be made available at http://servers.binf.ku.dk/hemaexplorer/ Methods Raw Affymetrix microarray data from our own repository and public available databases were normalized and batch corrected to build an integrated gene expression database for a series of normal hematopoietic cells and AML patient samples, at progressing stages of differentiation, which can be visualized directly or compared to external samples added by the user. A complete database of internal and user-supplied samples is build at each run of the analysis, using uniform transformation and correction parameters adjusted to ensure full integrity and comparability across all samples. The microarray database includes 44 highly purified sorted human normal blood samples and BM populations including HSCs, myeloid HPCs and their progeny, as well as mature cells of the innate and adaptive immune system. 10 samples were from public sources. In addition, our database includes microarray data from multiple AML studies (> 1000 samples across platforms) allowing for comparison of gene expression in WHO defined AML subclasses and normal hematopoietic cells. Results The main strength of the data-driven HemaExplorer 2.0 tool is the ability to quickly assess the main trends in how an AML sample diverges from normal cells during normal myeloid development. This can be accessed by specifying a gene of interest (Figure panel A-B. A user-supplied sample is marked in red in panel B) which provides interactive plots and hierarchical visualisations of gene expression where parameters including gene of interest, data source, and cell types can be selected and presented directly on the output figures usable for publications. Furthermore, a principal component analysis (PCA) plot can be performed, which allows for an unsupervised gene expression based mapping of user provided samples to the most closely related normal cell populations (figure panel C - here shown with cell lines commonly used in AML research). Discussion Several websites offer visualisation of gene expression in cells from the hematopoietic system, including Gene Expression Atlas (Nucl. Acids Res., 40, D1077–D1081) and our own HemaExplorer (Blood, 119(26), 6394-5 and Nucl. Acids Res. 41, D1034-D1039), without the possibility of external sample addition provided by the users. Gene Expression Commons (PLoS ONE 7(7), e40321) provides this option for public data, based on a common expression model. Here we offer the ability to add and compare unpublished microarray gene expression profiles to various types of normal blood and BM populations, in a ready-to-use platform normalized on single sample level, independently on the overall distribution of expression in a selected set of reference samples. Future efforts will include the ability to provide a standard differential expression analysis, comparing the user-supplied sample with a selection of the normal hematopoietic hierarchy. Furthermore, we aim to be able to offer a standalone version of the tool, which can be implemented internally on hospital servers, and expand the list of accepted microarray platforms. Disclosures: No relevant conflicts of interest to declare.

Download Full-text

Expansion of signaling genes for adaptive immune system evolution in early vertebrates

BMC Genomics ◽

10.1186/1471-2164-9-218 ◽

2008 ◽

Vol 9 (1) ◽

pp. 218 ◽

Cited By ~ 7

Author(s):

Kinya Okada ◽

Kiyoshi Asai

Keyword(s):

Immune System ◽

Adaptive Immune System ◽

System Evolution ◽

Adaptive Immune ◽

Immune System Evolution ◽

Early Vertebrates

Download Full-text

Interferon-Gamma Induced Changes in Gene Expression Dramatically Alter Neutrophil Phenotype

Blood ◽

10.1182/blood-2018-99-115314 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 2398-2398

Author(s):

Michael Ellison ◽

Natalie Briones ◽

Angelina Baroffio ◽

John Murphy ◽

Katherine Gowan ◽

...

Keyword(s):

Gene Expression ◽

Immune System ◽

Interferon Gamma ◽

Superoxide Anion ◽

Adaptive Immune System ◽

Neutrophil Function ◽

Superoxide Anion Generation ◽

Adaptive Immune ◽

Ifn Γ ◽

Dose Dependent

Abstract Interferon-gamma (IFN-γ) is a cytokine with powerful immunoregulatory effects. Most of these have been documented within the adaptive immune system and less has been reported about its effects on neutrophil function. Furthermore, most neutrophil studies have evaluated the effect of IFN- γ on mature cells isolated from peripheral blood thus potentially missing effects induced by its action on maturing neutrophils in the bone marrow. The clinical use of IFN-γ has been driven by these data and the clinical findings that administration of this cytokine to patients with Chronic Granulomatous Disease results in decreased incidence of severe infections without correcting the defect in phagocyte Nox2 activity. To determine the in vivo effects on neutrophils maturing in the marrow under the influence of this cytokine, we studied healthy human volunteers receiving IFN-γ at single escalating doses of 10, 25, 50, and 100 mcg/m2. Blood samples were obtained before and 4, 8, 12, 24, 36, 48, 72, and 96 hours after the administration. Plasma was stored for IFN-γ, IL-10 and neopterin determination by ELISA. Additionally, neutrophils were isolated from heparinized whole blood and superoxide anion generation after stimulation with PMA (200 ng/ml) and fMLF (1µM) was measured as SOD inhibitable cytochrome c reduction. RNA was isolated from neutrophils by standard techniques and genome wide changes in transcription were measured using Affymetrix gene chips. IFN-gamma concentrations in plasma spiked transiently after its administration and the magnitude and persistence of the resulting peaks were dose dependent. Levels of IL-10 and neopterin, two molecules known to respond to IFN-g, also exhibited time and dose dependent increases in plasma levels albeit with different kinetics; IL-10 responded with sharp peaks similar to the IFN- profiles, but neopterin showed slower developing and longer lasting increases. Superoxide anion generation by neutrophils in response to fMLF and PMA was quantitatively enhanced early after administration of IFN-γ returning to baseline by the end of the observation period. The increase in the respiratory burst exhibited a dose response with a plateau at 50 mcg/m2. Marked changes in gene expression were noted and, using the criteria of a 2-fold change over baseline, 866 genes showed increases and 1909 genes exhibited decreases in expression. The changes occurred rapidly after administration returning back towards baseline by 24-36 hours. Both dose dependent increases and decreases were observed. As expected, a number of genes directly associated with neutrophil function were increased such as Nox2 components (CYBB, NCF1), Fc receptors (FCGR1A, FCGR1B), and innate immune receptors including TLR5, TLR8 and LY96. Strikingly, dramatic changes were noted in the genes for proteins in MHCII and MCHI systems, guanylate binding proteins, and the chemokine receptor, CXCR4. In addition, the expression of GTP Cyclohydrolase 1 (GCH1), a rate limiting enzyme in the tetrahydrobiopterin (BH4) biosynthetic pathway, was increased 18-fold after IFN-γ administration. Since BH4 is a cofactor in nitric oxide (NO) synthases we speculated that increased GCH1 could enhance NO production in neutrophils. The upregulation of this pathway in neutrophils was confirmed with a demonstration that NO generation in neutrophil lysates spiked from low levels to peak 4-8 hours after IFN administration before returning toward baseline after 36 hours. The generation of NO as well as other changes in the neutrophil phenotype may provide compensatory strategies to afford more robust function to the cell limited by genetic defects of CGD or other neutrophil dysfunction disorders. These results demonstrate that administration of IFN-γ enhances classic neutrophil function and also induces previously under or unappreciated neutrophil functions. Under the influence of IFN-γ, the neutrophil alters its functional phenotype to include novel strategies that enhance its role in host defense and interaction with the adaptive immune system. Understanding these effects of IFN- γ will help define its clinical effects in CGD and extend its possible uses to other diseases. Disclosures Ambruso: Horizon Pharma Ireland Ltd: Other: Educational Consulting.

Download Full-text