scholarly journals Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Noah Dephoure ◽  
Sunyoung Hwang ◽  
Ciara O'Sullivan ◽  
Stacie E Dodgson ◽  
Steven P Gygi ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Redox Homeostasis ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Developmental Defects ◽  
Protein Levels ◽  
Cellular Processes ◽  
Universal Feature ◽  
Altered Metabolism ◽  
Encoding Genes

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms.

scholarly journals Class I Phosphoinositide 3-Kinase PIK3CA/p110α and PIK3CB/p110β Isoforms in Endometrial Cancer

2018 ◽  
Vol 19 (12) ◽  
pp. 3931 ◽  
Author(s):  
Fatemeh Mazloumi Gavgani ◽  
Victoria Smith Arnesen ◽  
Rhîan Jacobsen ◽  
Camilla Krakstad ◽  
Erling Hoivik ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Gene Copy Number ◽  
Biochemical Properties ◽  
Class I ◽  
Gene Copy ◽  
Gene Encoding ◽  
Cellular Processes ◽  
Pi3k Signalling ◽  
Phosphoinositide 3 Kinase ◽  
Phosphatase And Tensin Homologue

The phosphoinositide 3-kinase (PI3K) signalling pathway is highly dysregulated in cancer, leading to elevated PI3K signalling and altered cellular processes that contribute to tumour development. The pathway is normally orchestrated by class I PI3K enzymes and negatively regulated by the phosphatase and tensin homologue, PTEN. Endometrial carcinomas harbour frequent alterations in components of the pathway, including changes in gene copy number and mutations, in particular in the oncogene PIK3CA, the gene encoding the PI3K catalytic subunit p110α, and the tumour suppressor PTEN. PIK3CB, encoding the other ubiquitously expressed class I isoform p110β, is less frequently altered but the few mutations identified to date are oncogenic. This isoform has received more research interest in recent years, particularly since PTEN-deficient tumours were found to be reliant on p110β activity to sustain transformation. In this review, we describe the current understanding of the common and distinct biochemical properties of the p110α and p110β isoforms, summarise their mutations and highlight how they are targeted in clinical trials in endometrial cancer.

scholarly journals Human beta defensin (HBD) gene copy number affects HBD2 protein levels: impact on cervical bactericidal immunity in pregnancy

2018 ◽  
Vol 26 (3) ◽  
pp. 434-439 ◽  
Author(s):  
Catherine P. James ◽  
Mona Bajaj-Elliott ◽  
Razan Abujaber ◽  
Frida Forya ◽  
Nigel Klein ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Protein Levels ◽  
In Pregnancy

Gene copy number of epidermal growth factor receptor (EGFR) by fluorescent in situ hybridization (FISH) in head and neck squamous cell carcinomas (HNSCC) is closely correlated with EGFR protein levels assessed by automated quantitative protein analysis (AQUA)

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 6023-6023
Author(s):  
P. Weinberger ◽  
A. Psyrri ◽  
P. Kountourakis ◽  
T. Rampias ◽  
C. Sasaki ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Protein Expression ◽  
Protein Content ◽  
Gene Amplification ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Egfr Gene ◽  
Protein Levels

6023 Background: EGFR overexpression correlates with recurrence and with treatment resistance in HNSCC. The mechanisms of EGFR protein overexpression are poorly understood. Nonetheless, previous investigators have not demonstrated a correlation between EGFR gene copy number and protein content, using conventional immunohistochemistry (IHC). The aim of this study was to evaluate the relationship of EGFR gene copy number and protein expression utilizing fluorescence in situ hybridization (FISH) and AQUA, a novel, immunohistochemical method of automated quantitative in situ proteomic analysis which permits subcellular localization. Methods: A tissue microarray composed of 137 HNSCC treated with (chemo)radiation was constructed and analyzed for EGFR copy number by FISH (Vysis/Abbot) and EGFR protein expression (DAKO antibody) using AQUA analysis of EGFR staining scored on a scale of 0–255 and by conventional IHC. Agreement was assessed using kappa. Results: Sixteen (15%) of one-hundred six tumors with FISH results demonstrated EGFR high polysomy and/or gene amplification (FISH+). AQUA demonstrated a range of 3.6–102.2; protein levels assessed by AQUA in the FISH amplified cases were significantly higher (p =0.008) than in the FISH non- amplified ones. Using the EGFR 75th percentile as a cut-off, AQUA and FISH showed significant agreement (percentage of overall agreement 82%, kappa=0.458, p=0.003). To the contrary there was no concordance between FISH and conventional IHC results in this series. Conclusions: The discrepancy between EGFR gene amplification rate and protein expression by IHC reported previously may be due to the limitations and nonquantitative nature of conventional IHC. EGFR protein content correlates with gene copy number if protein content is quantitated and automatically analyzed, as with AQUA. No significant financial relationships to disclose.

scholarly journals mRNA detection in budding yeast with single fluorophores

2017 ◽  
Author(s):  
Gable M. Wadsworth ◽  
Rasesh Y. Parikh ◽  
John S. Choy ◽  
Harold D. Kim
Keyword(s):  
Single Molecule ◽  
Budding Yeast ◽  
Single Cells ◽  
Phenotypic Variability ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Mrna Levels ◽  
Protein Levels ◽  
Mrna Isoform

Quantitative measurement of mRNA levels in single cells is necessary to understand phenotypic variability within an otherwise isogenic population of cells. Single-molecule mRNA Fluorescence In Situ Hybridization (FISH) has been established as the standard method for this purpose, but current protocols require a long region of mRNA to be targeted by multiple DNA probes. Here, we introduce a new single-probe FISH protocol termed sFISH for budding yeast, Saccharomyces cerevisiae using a single DNA probe labeled with a single fluorophore. In sFISH, we markedly improved probe specificity and signal-to-background ratio by using methanol fixation and inclined laser illumination. We show that sFISH reports mRNA changes that correspond to protein levels and gene copy number. Using this new FISH protocol, we can detect more than 50% of the total target mRNA. We also demonstrate the versatility of sFISH using FRET detection and mRNA isoform profiling as examples. Our FISH protocol with single-fluorophore sensitivity significantly reduces cost and time compared to the conventional FISH protocols and opens up new opportunities to investigate small changes in RNA at the single cell level.

Evaluation of MET pathway biomarkers in a phase II study of rilotumumab (R, AMG 102) or placebo (P) in combination with epirubicin, cisplatin, and capecitabine (ECX) in patients (pts) with locally advanced or metastatic gastric (G) or esophagogastric junction (EGJ) cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 4005-4005 ◽  
Author(s):  
Kelly S. Oliner ◽  
Rui Tang ◽  
Abraham Anderson ◽  
Yun Lan ◽  
Timothy Iveson ◽  
...  
Keyword(s):  
Poor Prognosis ◽  
Human Monoclonal Antibody ◽  
Locally Advanced ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Double Blind ◽  
Protein Levels ◽  
Copy Numbers ◽  
Kaplan Meier ◽  
Cox Proportional Hazard Models

4005 Background: R is an investigational, fully human, monoclonal antibody to HGF/SF, the ligand of the MET receptor. A double-blind, P-controlled, phase 2 study randomized 121 G/EGJ cancer pts 1:1:1 to 15 mg/kg R + ECX (Arm A, n = 40), 7.5 mg/kg R + ECX (Arm B, n = 42), or P + ECX (Arm C, n = 39). OS and PFS improved with the addition of R to ECX (Iveson et al, European Multidisciplinary Cancer Congress 2011; abstr 6.504). High tumor MET levels have been associated with poor prognosis in G cancer (Nakajima et al, Cancer 1999;85:1894-1902). We explored MET pathway biomarkers to identify pts who may benefit from R. Methods: MET protein levels and gene copy numbers were measured in archival tumor samples by immunohistochemistry (IHC) and fluorescence in situ hybridization, respectively. High and low MET subgroups were defined by several predefined strategies. Total HGF and soluble MET (sMET) protein in plasma were measured by ELISA and MSD assays, respectively. Treatment and biomarker effects on OS and PFS were analyzed by Cox proportional hazard models and Kaplan-Meier estimates. Results: Tumor samples were evaluable for MET protein from 62 pts in Arms A + B and 28 pts in Arm C. Pts with METHigh tumors (> 50% tumor cells positive) in Arms A + B had improved median OS than those in Arm C (11.1 mo [80% CI: 9.2-13.3] vs 5.7 mo [80% CI: 4.5-10.4]; HR = 0.29, 95% CI: 0.11-0.76, p = 0.012). Conversely, pts with METLow tumors (≤ 50% positive) in Arms A + B had a trend toward unfavorable OS compared with those in Arm C (HR = 1.84, 95% CI: 0.78-4.34). In the chemotherapy only arm (Arm C), pts with METHigh tumors had poorer OS (HR = 3.22, 95% CI: 1.08-9.63) than pts with METLow tumors. Similar trends were seen with PFS. Predefined dichotomization schemes for tumor MET gene copy number and baseline plasma levels of total HGF or sMET did not correlate with OS or PFS. Conclusions: High MET expression by IHC may predict clinical benefit to R + ECX in G/EGJ cancer pts. High MET expression may also be associated with poor prognosis for ECX-treated pts. Further investigation is needed to confirm these findings.

Heuristic Modularity for Complex Identification in Protein-Protein Interaction Networks

2019 ◽  
pp. 1846-1859
Author(s):  
Amenah H. H. Abdulateef ◽  
Bara'a A. Attea ◽  
Ahmed N. Rashid
Keyword(s):  
Protein Interaction ◽  
Protein Complexes ◽  
Building Blocks ◽  
Detection Accuracy ◽  
Protein Protein Interaction ◽  
Protein Levels ◽  
Cellular Processes ◽  
Ppi Networks ◽  
Protein Protein Interaction Networks ◽  
Different Levels

     Due to the significant role in understanding cellular processes, the decomposition of Protein-Protein Interaction (PPI) networks into essential building blocks, or complexes, has received much attention for functional bioinformatics research in recent years. One of the well-known bi-clustering descriptors for identifying communities and complexes in complex networks, such as PPI networks, is modularity function.   The contribution of this paper is to introduce heuristic optimization models that can collaborate with the modularity function to improve its detection ability. The definitions of the formulated heuristics are based on nodes and different levels of their neighbor properties.  The modularity function and the formulated heuristics are then injected into the mechanism of a single objective Evolutionary Algorithm (EA) tailored specifically to tackle the problem, and thus, to identify possible complexes from PPI networks. In the experiments, different overlapping scores are used to evaluate the detection accuracy in both complex and protein levels. According to the evaluation metrics, the results reveal that the introduced heuristics have the ability to harness the accuracy of the existing modularity while identifying protein complexes in the tested PPI networks.

scholarly journals An EGR2/CITED1 Transcription Factor Complex and the 14-3-3σ Tumor Suppressor Are Involved in Regulating ErbB2 Expression in a Transgenic-Mouse Model of Human Breast Cancer

2007 ◽  
Vol 27 (24) ◽  
pp. 8648-8657 ◽  
Author(s):  
Rachelle L. Dillon ◽  
Stephen T. Brown ◽  
Chen Ling ◽  
Toshishiro Shioda ◽  
William J. Muller
Keyword(s):  
Transcription Factor ◽  
Tumor Suppressor ◽  
Gene Copy Number ◽  
Tumor Formation ◽  
Gene Copy ◽  
Mammary Tissue ◽  
Breast Cancers ◽  
Human Breast ◽  
Specific Expression ◽  
Protein Levels

ABSTRACT Amplification and elevated expression of the ErbB2 receptor tyrosine kinase occurs in 20% of human breast cancers and is associated with a poor prognosis. We have previously demonstrated that mammary tissue-specific expression of activated ErbB2 under the control of its endogenous promoter results in mammary tumor formation. Tumor development was associated with amplification and overexpression of ErbB2 at both the transcript and protein levels. Here we demonstrate that the EGR2/Krox20 transcription factor and its coactivator CITED1 are coordinately upregulated during ErbB2 tumor induction. We have identified an EGR2 binding site in the erbB2 promoter and demonstrated by chromatin immunoprecipitation assays that EGR2 and CITED1 associate specifically with this region of the promoter. EGR2 and CITED1 were shown to associate, and expression from an erbB2 promoter-reporter construct was stimulated by EGR2 and was further enhanced by CITED1 coexpression. Furthermore, expression of the 14-3-3σ tumor suppressor led to downregulation of ErbB2 protein levels and relocalization of EGR2 from the nucleus to the cytoplasm. Taken together, these observations suggest that, in addition to an increased gene copy number and upregulation of EGR2 and CITED1, an elevated erbB2 transcript level involves the loss of 14-3-3σ, which sequesters a key transcriptional regulator of the erbB2 promoter.

scholarly journals Gene Copy Number and Post-Transductional Mechanisms Regulate TRAP1 Expression in Human Colorectal Carcinomas

2019 ◽  
Vol 21 (1) ◽  
pp. 145 ◽  
Author(s):  
Michele Pietrafesa ◽  
Francesca Maddalena ◽  
Luciana Possidente ◽  
Valentina Condelli ◽  
Pietro Zoppoli ◽  
...  
Keyword(s):  
Copy Number ◽  
Molecular Mechanisms ◽  
Tumor Necrosis Factor Receptor ◽  
Gene Copy Number ◽  
Protein S ◽  
Lymph Node Involvement ◽  
The Cancer Genome Atlas ◽  
Gene Copy ◽  
Colorectal Carcinomas ◽  
Protein Levels

Tumor Necrosis Factor Receptor-Associated Protein 1 (TRAP1) is a heat shock protein 90 (HSP90) molecular chaperone overexpressed in 60–70% human colorectal carcinomas (CRCs) and the co-upregulation of TRAP1 and associated 6-related proteins identifies metastatic CRCs with poor prognosis. Since the molecular mechanisms responsible for TRAP1 regulation are still unknown, the significance of TRAP1 gene copy number (CN) and the role of post-transductional protein modifications were addressed. TRAP1 gene aneuploidy accounted for 34.5% of cases in a cohort of 58 human CRCs and TRAP1 CN correlated with its mRNA and protein expression, suggesting that transcriptional mechanisms are responsible for TRAP1 upregulation. Furthermore, the analysis of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium/The Cancer Genome Atlas (CPTAC/TCGA) CRC database showed that TRAP1 polysomy significantly correlates with lymph node involvement. However, a subgroup of tumors showed TRAP1 protein levels independent from its CN. Of note, a direct correlation was observed between TRAP1 protein levels and the expression of S-nitrosoglutathione reductase (GSNOR), a denitrosylase involved in the regulation of protein S-nitrosylation. Furthermore, CRC cell lines exposed to hypoxia or dichloroacetate treatment showed the downregulation of TRAP1 upon GSNOR silencing and this resulted in increased TRAP1 mono/polyubiquitination. These data suggest that transcriptional and post-transductional mechanisms account for TRAP1 expression in human CRCs and GSNOR protects TRAP1 from S-nitrosylation and consequent proteasome degradation mostly in conditions of stress.

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