27 research outputs found
Prediction of a Missing Protein Expression Map in the Context of the Human Proteome Project
Experimental evidence for the entire
human proteome has been defined
in the Human Proteome Project, and it is publicly available in the
neXtProt database. However, there are still human proteins for which
reliable experimental evidence does not exist, and the identification
of such information has become one of the overriding objectives in
the chromosome-centric study of the human proteome. With this aim
and considering the complexity of protein detection using shotgun
and targeted proteomics, the research community has addressed the
integration of transcriptomics and proteomics landscapes. Here, we
describe an analytical pipeline that predicts the probability of a
missing protein being expressed in a biological sample based on (1)
gene sequence characteristics, (2) the probability of an expressed
gene being a coding gene of a missing protein in a certain sample,
and (3) the probability of a gene being expressed in a transcriptomic
experiment. More than 3400 microarray experiments were analyzed corresponding
to three biological sources: cell lines, normal tissues, and cancer
samples. A gene classification based on gene expression profiles distinguished
among ubiquitous, nonubiquitous, nonexpressed, and coding genes of
missing proteins. In addition, a different tissue-specific expression
pattern for the coding genes of missing proteins is reported. Our
results underline the relevance of selecting an appropriate sample
for the detection of missing proteins and provide a comprehensive
method to score their expression probability. Testis, brain, and skeletal
muscle are the most promising normal tissues
Proteome of the Early Embryo–Maternal Dialogue in the Cattle Uterus
We analyzed embryo–maternal interactions in the
bovine uterus
on day 8 of development. Proteomic profiles were obtained by two-dimensional
difference gel electrophoresis from 8 paired samples of uterine fluid
(UF) from the same animal with and without embryos in the uterus.
Results were contrasted with UF obtained after artificial insemination.
We detected 50 differential protein spots (<i>t</i> test, <i>p</i> < 0.05). Subsequent protein characterization by nano-LC–ESI–MS/MS
enabled us to identify 38 proteins, obtaining for first time the earliest
evidence of involvement of the down-regulated NFkB system in cattle
as a pregnancy signature pathway. Embryos enhanced the embryotrophic
ability of UF and decreased uterine protein, while blood progesterone
was unaltered. Twinfilin, hepatoma-derived growth factor, and synaptotagmin-binding
cytoplasmic RNA interacting protein have not previously been identified
in the mammalian uterus. TNFα and IL-1B were localized to embryos
by immunocytochemistry, and other proteins were validated by Western
blot in UF. Glycosylated-TNFα, IL-1B, insulin, lactotransferrin,
nonphosphorylated-peroxiredoxin, albumin, purine nucleoside phosphorylase,
HSPA5, and NFkB were down-regulated, while phosphorylated-peroxiredoxin,
annexin A4, and nonglycosylated-TNFα were up-regulated. The
embryonic signaling agents involved could be TNFα and IL-1B,
either alone or in a collective dialogue with other proteins. Such
molecules might explain the immune privilege during early bovine development
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
The Human Proteome
Project (HPP) aims deciphering the complete
map of the human proteome. In the past few years, significant efforts
of the HPP teams have been dedicated to the experimental detection
of the missing proteins, which lack reliable mass spectrometry evidence
of their existence. In this endeavor, an in depth analysis of shotgun
experiments might represent a valuable resource to select a biological
matrix in design validation experiments. In this work, we used all
the proteomic experiments from the NCI60 cell lines and applied an
integrative approach based on the results obtained from Comet, Mascot,
OMSSA, and X!Tandem. This workflow benefits from the complementarity
of these search engines to increase the proteome coverage. Five missing
proteins C-HPP guidelines compliant were identified, although further
validation is needed. Moreover, 165 missing proteins were detected
with only one unique peptide, and their functional analysis supported
their participation in cellular pathways as was also proposed in other
studies. Finally, we performed a combined analysis of the gene expression
levels and the proteomic identifications from the common cell lines
between the NCI60 and the CCLE project to suggest alternatives for
further validation of missing protein observations
Embryonic Sex Induces Differential Expression of Proteins in Bovine Uterine Fluid
The bovine endometrium recognizes early embryos and reacts
differently
depending on the developmental potential of the embryo. However, it
is unknown whether the endometrium can distinguish embryonic sex.
Our objective was to analyze sexual dimorphism in the uterus in response
to male and female embryos. Differentially expressed (DE) proteins,
different levels of hexoses, and other embryotrophic differences were
analyzed in uterine fluid (UF). Proteomic analysis of day-8 UF recovered
from heifers after the transfer of day-5 male or female embryos identified
23 DE proteins. Regulated proteasome/immunoproteasome protein subunits
indicated differences in antigen processing between UF carrying male
embryos (male-UF) or female embryos (female-UF). Several enzymes involved
in glycolysis/gluconeogenesis and antioxidative/antistress responses
were up-regulated in female-UF. Fructose concentration was increased
in female-UF versus male-UF, while glucose levels were similar. <i>In vitro</i> cultures with molecules isolated from male-UF were
found to improve male embryo development compared to female embryos
cultured with molecules isolated from female-UF. We postulated that, <i>in vivo</i>, male embryos induce changes in the endometrium
to help ensure their survival. In contrast, female embryos do not
appear to induce these changes
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence
The current catalogue of the human
proteome is not yet complete,
as experimental proteomics evidence is still elusive for a group of
proteins known as the missing proteins. The Human Proteome Project
(HPP) has been successfully using technology and bioinformatic resources
to improve the characterization of such challenging proteins. In this
manuscript, we propose a pipeline starting with the mining of the
PRIDE database to select a group of data sets potentially enriched
in missing proteins that are subsequently analyzed for protein identification
with a method based on the statistical analysis of proteotypic peptides.
Spermatozoa and the HEK293 cell line were found to be a promising
source of missing proteins and clearly merit further attention in
future studies. After the analysis of the selected samples, we found
342 PSMs, suggesting the presence of 97 missing proteins in human
spermatozoa or the HEK293 cell line, while only 36 missing proteins
were potentially detected in the retina, frontal cortex, aorta thoracica,
or placenta. The functional analysis of the missing proteins detected
confirmed their tissue specificity, and the validation of a selected
set of peptides using targeted proteomics (SRM/MRM assays) further
supports the utility of the proposed pipeline. As illustrative examples,
DNAH3 and TEPP in spermatozoa, and UNCX and ATAD3C in HEK293 cells
were some of the more robust and remarkable identifications in this
study. We provide evidence indicating the relevance to carefully analyze
the ever-increasing MS/MS data available from PRIDE and other repositories
as sources for missing proteins detection in specific biological matrices
as revealed for HEK293 cells
Oral administration of MTA to <i>Mdr2<sup>−/−</sup></i> mice reduces hepatomegaly and serum parameters of liver injury.
<p><i>Mdr2<sup>+/+</sup></i> and <i>Mdr2<sup>−/−</sup></i> mice were treated with MTA during three weeks. Increased liver-to-body weight ratio (%) in <i>Mdr2<sup>−/−</sup></i> mice was reduced by MTA (A). Serum transaminases (B), alkaline phosphatase (C) and bilirubin (D), levels that are increased in <i>Mdr2<sup>−/−</sup></i> mice were attenuated by MTA. *<i>P</i><0.05 <i>vs</i> untreated <i>Mdr2<sup>+/+</sup></i> mice, #<i>P</i><0.05 <i>vs</i> untreated <i>Mdr2<sup>−/−</sup></i> mice.</p
Potential mechanisms of action of MTA in <i>Mdr2<sup>−/−</sup></i> mice.
<p>Our <i>in vivo</i> and <i>in vitro</i> observations indicate that MTA displays different actions that may underlie its beneficial effects on the course of liver injury and fibrosis in <i>Mdr2<sup>−/−</sup></i> mice. MTA may exert a direct cytoprotective effect on hepatocytes by reducing JNK activity, preventing hepatocellular death and further inflammation. MTA also inhibits the production of cytokines by inflammatory cells, likely through interference with NFκB activity as described before <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015690#pone.0015690-Hevia1" target="_blank">[16]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015690#pone.0015690-IglesiasAra1" target="_blank">[18]</a>. In addition, enhanced expression of adenosine A2B receptors may contribute to the anti-inflammatory pharmacological profile of MTA. This compound can also exert direct effects on extracellular matrix (ECM) producing cells (myofibroblasts), reducing their activation, proliferation and the production of pro-fibrogenic factors. Inhibition of JunD expression may be an important event in the antifibrogenic action of MTA.</p
Expression of fibrogenic activation and cellular proliferation-related genes in myofibroblasts isolated from the liver of control and MTA-treated <i>Mdr2−/−</i> mice.
<p><i>Mdr2−/−</i> mice were treated for three weeks with MTA or vehicle as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015690#s2" target="_blank">Methods</a> section. At the end of the treatments hepatic myofibroblasts were isolated and the mRNA levels of the indicated genes were measured. Data are means ±SEM of three independent cell preparations per condition. *<i>P</i><0.05 <i>vs</i> vehicle-treated <i>Mdr2−/−</i> mice.</p
Effects of MTA on liver myofibroblast activation and cytokine expression.
<p>Primary myofibroblasts were serum starved (12 h) and then treated (12 h) with 10% FCS and MTA as indicated. mRNA levels of α1(I)procollagen (A), αSMA (B), TGFβ1 (C), TGFβ2 (D), Mcp-1 (E) and IL6 (F) were measured at the end of treatments. *<i>P</i><0.05 <i>vs</i> FCS, #<i>P</i><0.05 <i>vs</i> FCS+MTA 200 µM.</p
MTA modulates intracellular signalling pathways activated in <i>Mdr2<sup>−/−</sup></i> mouse liver.
<p>Phosphorylation levels of Smad1/5/8 (A), Smad2 (B), JNK and c-Jun (C) and Erk1/2 (D) were analyzed by western blotting in liver extracts from <i>Mdr2<sup>+/+</sup></i>, control <i>Mdr2<sup>−/−</sup></i>, and MTA-treated <i>Mdr2<sup>−/−</sup></i> mice. *<i>P</i><0.05 <i>vs Mdr2<sup>+/+</sup></i> mice, #<i>P</i><0.05 <i>vs</i> untreated <i>Mdr2<sup>−/−</sup></i> mice.</p