scholarly journals Comprehensive immune transcriptomic analysis in bladder cancer reveals subtype specific immune gene expression patterns of prognostic relevance

Oncotarget ◽  
2017 ◽  
Vol 8 (41) ◽  
pp. 70982-71001 ◽  
Author(s):  
Runhan Ren ◽  
Kathrin Tyryshkin ◽  
Charles H. Graham ◽  
Madhuri Koti ◽  
D. Robert Siemens
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Expression Patterns ◽  
Transcriptomic Analysis ◽  
Gene Expression Patterns ◽  
Immune Gene ◽  
Immune Gene Expression ◽  
Prognostic Relevance

scholarly journals Environmental rearing conditions are key determinants of changes in immune gene expression patterns in shrimp midgut

2020 ◽  
Vol 106 ◽  
pp. 103618
Author(s):  
Mariana Rangel Pilotto ◽  
Nicolas Argenta ◽  
Jamille Martins Forte ◽  
Bárbara Hostins ◽  
Francisca Gleire R. Menezes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Immune Gene ◽  
Immune Gene Expression ◽  
Rearing Conditions

scholarly journals Dissecting the contributions of time and microbe density to variation in immune gene expression

2017 ◽  
Vol 284 (1859) ◽  
pp. 20170727 ◽  
Author(s):  
Ann T. Tate ◽  
Andrea L. Graham
Keyword(s):  
Gene Expression ◽  
Functional Outcomes ◽  
Expression Patterns ◽  
Immune Gene ◽  
Cross Sectional ◽  
Underlying Assumption ◽  
Temporal Gene Expression ◽  
Immune Gene Expression ◽  
Highly Correlated ◽  
Almost All

Widespread differential expression of immunological genes is a hallmark of the response to infection in almost all surveyed taxa. However, several challenges remain in the attempt to connect differences in gene expression with functional outcomes like parasite killing and host survival. For example, temporal gene expression patterns are not always monotonic (unidirectional slope), yielding results that qualitatively depend on the time point selected for analysis. They may also be correlated to microbe density, confounding the strength of an immune response and resistance to parasites. In this study, we analyse these relationships in an mRNA-seq time series of Tribolium castaneum infected with Bacillus thuringiensis . Our results suggest that many extracellular immunological components with known roles in immunity, like antimicrobial peptides and recognition proteins, are highly correlated to microbe load. On the other hand, intracellular components of immunological signalling pathways overwhelmingly show non-monotonic temporal patterns of gene expression, despite the underlying assumption of monotonicity in most ecological and comparative transcriptomics studies that rely on cross-sectional analyses. Our results raise a host of new questions, including to what extent variation in host resistance, infection tolerance and immunopathology can be explained by variation in the slope or sensitivity of these newly characterized patterns.

scholarly journals Immune gene expression profiling reveals heterogeneity in luminal breast tumors

2019 ◽  
Author(s):  
Bin Zhu ◽  
Shelly Lap Ah Tse ◽  
Difei Wang ◽  
Hela Koka ◽  
Tongwu Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Gene Expression Profiling ◽  
T Cell Activation ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Luminal Breast Cancer ◽  
Immune Gene ◽  
Disease Heterogeneity ◽  
Immune Gene Expression

AbstractDisease heterogeneity of immune gene expression patterns of luminal breast cancer (BC) has not been well studied. We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 Asian luminal BC patients and identified three distinct immune subtypes. Tumors in one subtype exhibited signs of T-cell activation, lower ESR1/ESR2 expression ratio and higher expression of immune checkpoint genes, nonsynonymous mutation burden, APOBEC-signature mutations, and increasing body mass index compared to other luminal tumors. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in cases drawn from The Cancer Genome Atlas and a Korean breast cancer study. Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification.

Hedgehog gene expression patterns among intrinsic subtypes of breast cancer: prognostic relevance

2021 ◽  
pp. 153478
Author(s):  
Araceli García-Martínez ◽  
Ariadna Pérez-Balaguer ◽  
Fernando Ortiz-Martínez ◽  
Eloy Pomares-Navarro ◽  
Elena Sanmartín ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Intrinsic Subtypes ◽  
Prognostic Relevance

scholarly journals Biofilm Produced In Vitro by Piscirickettsia salmonis Generates Differential Cytotoxicity Levels and Expression Patterns of Immune Genes in the Atlantic Salmon Cell Line SHK-1

2020 ◽  
Vol 8 (10) ◽  
pp. 1609
Author(s):  
Natacha Santibañez ◽  
Matías Vega ◽  
Tatiana Pérez ◽  
Alejandro Yáñez ◽  
Roxana González-Stegmaier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atlantic Salmon ◽  
Cell Line ◽  
Biofilm Formation ◽  
Expression Patterns ◽  
Host Cells ◽  
Immune Gene ◽  
Immune Gene Expression ◽  
Piscirickettsia Salmonis

Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, an infectious disease with a high economic impact on the Chilean salmonid aquaculture industry. This bacterium produces biofilm as a potential resistance and persistence strategy against stressful environmental stimuli. However, the in vitro culture conditions that modulate biofilm formation as well as the effect of sessile bacteria on virulence and immune gene expression in host cells have not been described for P. salmonis. Therefore, this study aimed to analyze the biofilm formation by P. salmonis isolates under several NaCl and iron concentrations and to evaluate the virulence of planktonic and sessile bacteria, together with the immune gene expression induced by these bacterial conditions in an Atlantic salmon macrophage cell line. Our results showed that NaCl and Fe significantly increased biofilm production in the LF-89 type strain and EM-90-like isolates. Additionally, the planktonic EM-90 isolate and sessile LF-89 generated the highest virulence levels, associated with differential expression of il-1β, il-8, nf-κb, and iκb-α genes in SHK-1 cells. These results suggest that there is no single virulence pattern or gene expression profile induced by the planktonic or sessile condition of P. salmonis, which are dependent on each strain and bacterial condition used.

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