Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii

The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water, in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.

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Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii

10.7287/peerj.preprints.642 ◽

2014 ◽

Author(s):

Jean-Christophe Avarre ◽

Bruno Guinand ◽

Rémi Dugué ◽

Jacky Cosson ◽

Marc Legendre ◽

...

Keyword(s):

Gene Expression ◽

Natural Habitat ◽

Expression Patterns ◽

Osmotic Tolerance ◽

Two Generations ◽

Hypersaline Water ◽

Significant Expression ◽

Physiological Impact ◽

High Level ◽

Sarotherodon Melanotheron

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Diabetes-specific modulation of peripheral blood gene expression signatures in colorectal cancer

Current Molecular Medicine ◽

10.2174/1566524020666200504084626 ◽

2020 ◽

Vol 20 ◽

Author(s):

Zsuzsanna Molnár ◽

Zsófia Bánlaki ◽

Anikó Somogyi ◽

Zoltán Herold ◽

Magdolna Herold ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Expression Patterns ◽

Enrichment Analysis ◽

Colorectal Carcinogenesis ◽

Differentially Expressed ◽

Blood Leukocytes ◽

Significant Expression

Background: Type 2 diabetes (T2DM) and colorectal cancer (CRC) are both known to modulate gene expression patterns in peripheral blood leukocytes (PBLs). Objective : As T2DM has been shown to increase the incidence of CRC, we were prompted to check whether diabetes affects mRNA signatures in PBLs isolated from CRC patients. Methods : 22 patients were recruited to the study and classified into four cohorts (healthy controls; T2DM; CRC; CRC and T2DM). Relative expression levels of 573 cell signaling gene transcripts were determined by reverse transcription real-time PCR assays run on low-density OpenArray platforms. Enrichment analysis was performed with the g:GOSt profiling tool to order differentially expressed genes into functional pathways. Results : 49 genes were found to be significantly up- or downregulated in tumorous diabetic individuals as compared to tumor-free diabetic controls, while 11 transcripts were differentially regulated in patients with CRC versus healthy, tumor-free and non-diabetic controls. Importantly, these gene sets were completely distinct, implying that diabetes exerts profound influence on the transcription of signaling genes in CRC. The top 5 genes showing most significant expression differences in both contexts were PCK2, MAPK9, CCND1, HMBS, TLR3 (p≤ 0.0040) and CREBBP, PPIA, NFKBIL1, MDM2 and SELPLG (p0.0121), respectively. Functional analysis revealed that most significantly affected pathways were cytokine, interleukin and PI3K/Akt/mTOR signaling cascades as well as mitotic regulation. Conclusions : We propose that differentially expressed genes listed above might be potential biomarkers of CRC and should be studied further on larger patient groups. Diabetes might promote colorectal carcinogenesis by impairing signaling pathways in PBLs.

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High level analysis of genomic data reveals complex predictors of response to trastuzumab (T) and chemotherapy for early stage breast cancer

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.544 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 544-544

Author(s):

L. N. Harris ◽

S. Carter ◽

F. You ◽

A. Eklund ◽

S. Hilsenbeck ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Expression Patterns ◽

Rna Extraction ◽

Pathologic Complete Response ◽

Gene Expression Signature ◽

Response To Therapy ◽

Snp Analysis ◽

Predictors Of Response ◽

High Level

544 Background: Trastuzumab (T) with chemotherapy has been shown to improve survival in breast cancer patients but de novo resistance is common. Identifying predictors of response to T in primary cancers may lead to an understanding of mechanisms of resistance. We investigated whether combined microarray datasets from patients with early breast cancer treated with preoperative T and chemotherapy could predict for response to therapy. Methods: Two cohorts of patients with HER2 3+/FISH+, stage II-III breast cancer were included in this analysis: trial 1- T and docetaxel (n=38), trial 2 -T and vinorelbine (n=48), both for 12 weeks. Frozen tissue core biopsies were available and successfully amplified in 41 patients (trial 1: 20, trial 2: 21 patients), with standard sample processing, RNA extraction, amplification and hybridization to Affymetrix U133 chips. Differential expression of genes and chromosomal regions, (defined as >10 genes in a given chromosomal cytoband), between patients with pathologic complete response (pCR) vs. those with residual invasive disease were examined. A measure of total functional aneuploidy (tFA) was calculated by summing net deviation in expression of all chromosomal regions and a gene expression signature of genomic instability (CIN) was derived by the identification of genes showing a high level of correlation with tFA . Results: By unsupervised hierarchical analysis, both datasets interdigitated suggesting no inherent bias. Gene expression patterns of individual genes showed weak associations with pCR. However, distinct statistically significant chromosomal regions, Chr2p23 Chr6q24 Chr7q33 Chr2p2 Chr12q21.31 Chr14q32.2 Chr1p34.2 Chr8q21.3, were associated with pCR to T therapy (p<0.005), and were confirmed in more than 50% samples by SNP analysis. In addition, resistant tumors showed higher levels of the CIN signature (p<0.005). Conclusions: We have shown that gene expression data can be merged and used for discovery predictive chromosomal regions associated T response. In addition, chromosomal instability was associated with T resistance. If validated, these distinct dysregulated chromosomal regions may serve as predictive markers of response to trastuzumab therapy. [Table: see text]

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Patterns of Expression of a Lolitrem Biosynthetic Gene in the Epichloë festucae–Perennial Ryegrass Symbiosis

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-21-2-0188 ◽

2008 ◽

Vol 21 (2) ◽

pp. 188-197 ◽

Cited By ~ 14

Author(s):

Kimberley J. May ◽

Michelle K. Bryant ◽

Xiuwen Zhang ◽

Barbara Ambrose ◽

Barry Scott

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Expression Patterns ◽

In Planta ◽

Temporal Expression ◽

Epichloë Festucae ◽

Gusa Reporter Gene ◽

Reporter Gene Analysis ◽

High Level ◽

Germinating Seeds

Lolitrem B is synthesized by Epichloë festucae in associations with Pooid grasses. A complex cluster of at least 10 genes (ltm genes) is required for its synthesis. An early step in this pathway is catalyzed by ltmM, a symbiosis-expressed gene. PltmM-gusA reporter gene analysis was used to monitor ltmM gene expression patterns in planta. The minimum promoter length required for high-level gusA expression in infected seedlings is in the range of 480 to 782 bp. gusA was expressed by the endophyte in all infected vegetative plant tissues and in epiphyllous hyphae. Spikelets from reproductive tillers were analyzed at different developmental stages. During pre-anthesis, gusA expression was observed in all infected floral organs except the immature gynoecium. In post-anthesis florets, gene expression occurred almost exclusively in the gynoecium. Expression of gusA by the endophyte was observed in germinating seeds 24 h postimbibition and seedlings older than 6 days postimbibition in hyphae from the mesocotyl to the tip of the emerging first leaf. This work provides a detailed analysis of the spatial and temporal expression patterns of a symbiosis-expressed gene in planta.

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A nuclear glutathione cycle within the cell cycle

Biochemical Journal ◽

10.1042/bj20100409 ◽

2010 ◽

Vol 431 (2) ◽

pp. 169-178 ◽

Cited By ~ 150

Author(s):

Pedro Diaz Vivancos ◽

Tonja Wolff ◽

Jelena Markovic ◽

Federico V. Pallardó ◽

Christine H. Foyer

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Nuclear Dna ◽

Expression Patterns ◽

Animal Cells ◽

Cellular Redox ◽

Intracellular Compartments ◽

Glutathione Cycle ◽

Defence Proteins ◽

High Level

The complex antioxidant network of plant and animal cells has the thiol tripeptide GSH at its centre to buffer ROS (reactive oxygen species) and facilitate cellular redox signalling which controls growth, development and defence. GSH is found in nearly every compartment of the cell, including the nucleus. Transport between the different intracellular compartments is pivotal to the regulation of cell proliferation. GSH co-localizes with nuclear DNA at the early stages of proliferation in plant and animal cells. Moreover, GSH recruitment and sequestration in the nucleus during the G1- and S-phases of the cell cycle has a profound impact on cellular redox homoeostasis and on gene expression. For example, the abundance of transcripts encoding stress and defence proteins is decreased when GSH is sequestered in the nucleus. The functions of GSHn (nuclear GSH) are considered in the present review in the context of whole-cell redox homoeostasis and signalling, as well as potential mechanisms for GSH transport into the nucleus. We also discuss the possible role of GSHn as a regulator of nuclear proteins such as histones and PARP [poly(ADP-ribose) polymerase] that control genetic and epigenetic events. In this way, a high level of GSH in the nucleus may not only have an immediate effect on gene expression patterns, but also contribute to how cells retain a memory of the cellular redox environment that is transferred through generations.

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Analysis of transcription factor expression during oogenesis and preimplantation development in mice

Zygote ◽

10.1017/s096719940700411x ◽

2007 ◽

Vol 15 (2) ◽

pp. 117-128 ◽

Cited By ~ 15

Author(s):

S. Kageyama ◽

W. Gunji ◽

M. Nakasato ◽

Y. Murakami ◽

M. Nagata ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Germ Cell ◽

Expression Patterns ◽

Preimplantation Development ◽

Global Changes ◽

Regulation Of Transcription ◽

Cell Stage ◽

High Level ◽

And Function

SummaryThe transition from a differentiated germ cell into a totipotent zygote during oogenesis and preimplantation development is critical to the creation of a new organism. During this period, cell characteristics change dynamically, suggesting that a global alteration of gene expression patterns occurs, which is regulated by global changes in various epigenetic factors. Among these, transcription factors (TFs) are essential in the direct regulation of transcription and also play important roles in determining cell characteristics. However, no comprehensive analysis of TFs from germ cells to embryos had been undertaken. We used mRNA amplification systems and microarrays to conduct a genomewide analysis of TFs at various stages of oogenesis and preimplantation development. The greatest alteration in TFs occurred between the 1- and 2-cell stages, at which time zygotic genome activation (ZGA) occurs. Our analysis of TFs classified by structure and function revealed several specific patterns of change. Basic transcription factors, which are the general components of transcription, increased transiently at the 2-cell stage, while homeodomain (HD) TFs were expressed specifically in the oocyte. TFs containing the Rel homology region (RHR) and Ets domains were expressed at a high level in 2-cell and blastocyst embryos. Thus, the global TF dynamics that occur during oogenesis and preimplantation development seem to regulate the transition from germ-cell-type to embryo-type gene expression.

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The Prognostic Significance of Proteasome 26S Subunit, Non-ATPase (PSMD) Genes for Bladder Urothelial Carcinoma Patients

Cancer Informatics ◽

10.1177/11769351211067692 ◽

2021 ◽

Vol 20 ◽

pp. 117693512110676

Author(s):

AbdulFattah Salah Fararjeh ◽

Ali Al-Khader ◽

Malak Al-Saleem ◽

Rinad Abu Qauod

Keyword(s):

Gene Expression ◽

Urothelial Carcinoma ◽

Expression Patterns ◽

Mrna Level ◽

Prognostic Significance ◽

Progression Free Survival ◽

Normal Bladder ◽

Bladder Urothelial Carcinoma ◽

High Level ◽

Proteasome 26S

Proteasome a highly sophisticated systems that alter protein structure and function. Proteasome 26S Subunit, Non-ATPase (PSMD) genes have been implicated in several types of malignancies. This is the first study to look at how proteasomal subunits are expressed in patients with bladder urothelial carcinoma (BLCA). BLCA was used to evaluate the predictive value of PSMD genes (PSMD1 to PSMD12) in relation to clinicopathological characteristics. PSMD genes’ expression patterns at the mRNA level were analyzed using a variety of bioinformatics methods, including gene expression profile integrative analysis (GEPIA), Oncomine, TCGA, and Gene expression Omnibus (GEO) databases. The GEPIA and TCGA dataset survival plot functions were used to assess the prognostic significance of PSMD genes. PSMD2, PSMD3, PSMD4, PSMD8, and PSMD11 genes were significantly overexpressed in BLCA compared with normal bladder tissues. PSMD2 and PSMD8 were significantly overexpressed in BLCA more than other types of cancer. High level of PSMD2 and PSMD8 predicted shorter overall (OS) and progression free survival (PFS) in BLCA patients. High level of PSMD2 was significantly associated with elder age ( P < .001), female gender ( P = .014), tumor grade ( P < .001), and metastasis ( P = .003). PSMD2 has been shown to be an independent predictor for OS in BLCA patients based on univariate and multivariate analysis ( P < .001). Overall, according to this study, PSMD2 and PSMD8 could be served as a prognostic biomarker for BLCA patients.

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