9 research outputs found
Distinct Protein Expression Profiles of Solid-Pseudopapillary Neoplasms of the Pancreas
Solid-pseudopapillary neoplasm (SPN)
is an uncommon pancreatic
tumor with mutation in <i>CTNNB1</i> and distinct clinical
and pathological features. We compared the proteomic profiles of SPN
to mRNA expression. Pooled SPNs and pooled non-neoplastic pancreatic
tissues were examined with high-resolution mass spectrometry. We identified
329 (150 up-regulated and 179 down-regulated) differentially expressed
proteins in SPN. We identified 191 proteins (58.1% of the 329 dysregulated
proteins) with the same expression tendencies in SPN based on mRNA
data. Many overexpressed proteins were related to signaling pathways
known to be activated in SPNs. We found that several proteins involved
in Wnt signaling, including DKK4 and β-catenin, and proteins
that bind β-catenin, such as FUS and NONO, were up-regulated
in SPNs. Molecules involved in glycolysis, including PKM2, ENO2, and
HK1, were overexpressed in accordance to their mRNA levels. In summary,
SPN showed (1) distinct protein expression changes that correlated
with mRNA expression, (2) overexpression of Wnt signaling proteins
and proteins that bind directly to β-catenin, and (3) overexpression
of proteins involved in metabolism. These findings may help develop
early diagnostic biomarkers and molecular targets
Identification of Human Complement Factor B as a Novel Biomarker Candidate for Pancreatic Ductal Adenocarcinoma
Pancreatic cancer (PC; pancreatic
ductal adenocarcinoma) is characterized
by significant morbidity and mortality worldwide. Although carbohydrate
antigen (CA) 19-9 has been known as a PC biomarker, it is not commonly
used for general screening because of its low sensitivity and specificity.
Therefore, there is an urgent need to develop a new biomarker for
PC diagnosis in the earlier stage of cancer. To search for a novel
serologic PC biomarker, we carried out an integrated proteomic analysis
for a total of 185 pooled or individual plasma from healthy donors
and patients with five disease groups including chronic pancreatitis
(CP), PC, and other cancers (e.g., hepatocellular carcinoma, cholangiocarcinoma,
and gastric cancer) and identified complement factor b (CFB) as a
candidate serologic biomarker for PC diagnosis. Immunoblot analysis
of CFB revealed more than two times higher expression in plasma samples
from PC patients compared with plasma from individuals without PC.
Immunoprecipitation coupled to mass spectrometry analysis confirmed
both molecular identity and higher expression of CFB in PC samples.
CFB showed distinctly higher specificity than CA 19-9 for PC against
other types of digestive cancers and in discriminating PC patients
from non-PC patients (<i>p</i> < 0.0001). In receiver
operator characteristic curve analysis, CFB showed an area under curve
of 0.958 (95% CI: 0.956 to 0.959) compared with 0.833 (95% CI: 0.829
to 0.837) for CA 19-9. Furthermore, the Y-index of CFB was much higher
than that of CA 19-9 (71.0 vs 50.4), suggesting that CFB outperforms
CA 19-9 in discriminating PC from CP and other gastrointestinal cancers.
This was further supported by immunoprecipitation and qRT-PCR assays
showing higher expression of CFB in PC cell lines than in normal cell
lines. A combination of CFB and CA 19-9 showed markedly improved sensitivity
(90.1 vs 73.1%) over that of CFB alone in the diagnosis of PC against
non-PC, with similar specificity (97.2 vs 97.9%). Thus, our results
identify CFB as a novel serologic PC biomarker candidate and warrant
further investigation into a large-scale validation and its role in
molecular mechanism of pancreatic carcinogenesis
Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project
As a starting point of the Chromosome-Centric Human Proteome
Project
(C-HPP), we established strategies of genome-wide proteomic analysis,
including protein identification, quantitation of disease-specific
proteins, and assessment of post-translational modifications, using
paired human placental tissues from healthy and preeclampsia patients.
This analysis resulted in identification of 4239 unique proteins with
high confidence (two or more unique peptides with a false discovery
rate less than 1%), covering 21% of approximately 20 059 (Ensembl
v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially
expressed preeclampsia-specific proteins. When these proteins are
assigned to all human chromosomes, the pattern of the newly identified
placental protein population is proportional to that of the gene count
distribution of each chromosome. We also identified 219 unique <i>N</i>-linked glycopeptides, 592 unique phosphopeptides, and
66 chromosome 13-specific proteins. In particular, protein evidence
of 14 genes previously known to be specifically up-regulated in human
placenta was verified by mass spectrometry. With respect to the functional
implication of these proteins, 38 proteins were found to be involved
in regulatory factor biosynthesis or the immune system in the placenta,
but the molecular mechanism of these proteins during pregnancy warrants
further investigation. As far as we know, this work produced the highest
number of proteins identified in the placenta and will be useful for
annotating and mapping all proteins encoded in the human genome
Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project
As a starting point of the Chromosome-Centric Human Proteome
Project
(C-HPP), we established strategies of genome-wide proteomic analysis,
including protein identification, quantitation of disease-specific
proteins, and assessment of post-translational modifications, using
paired human placental tissues from healthy and preeclampsia patients.
This analysis resulted in identification of 4239 unique proteins with
high confidence (two or more unique peptides with a false discovery
rate less than 1%), covering 21% of approximately 20 059 (Ensembl
v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially
expressed preeclampsia-specific proteins. When these proteins are
assigned to all human chromosomes, the pattern of the newly identified
placental protein population is proportional to that of the gene count
distribution of each chromosome. We also identified 219 unique <i>N</i>-linked glycopeptides, 592 unique phosphopeptides, and
66 chromosome 13-specific proteins. In particular, protein evidence
of 14 genes previously known to be specifically up-regulated in human
placenta was verified by mass spectrometry. With respect to the functional
implication of these proteins, 38 proteins were found to be involved
in regulatory factor biosynthesis or the immune system in the placenta,
but the molecular mechanism of these proteins during pregnancy warrants
further investigation. As far as we know, this work produced the highest
number of proteins identified in the placenta and will be useful for
annotating and mapping all proteins encoded in the human genome
Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project
As a starting point of the Chromosome-Centric Human Proteome
Project
(C-HPP), we established strategies of genome-wide proteomic analysis,
including protein identification, quantitation of disease-specific
proteins, and assessment of post-translational modifications, using
paired human placental tissues from healthy and preeclampsia patients.
This analysis resulted in identification of 4239 unique proteins with
high confidence (two or more unique peptides with a false discovery
rate less than 1%), covering 21% of approximately 20 059 (Ensembl
v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially
expressed preeclampsia-specific proteins. When these proteins are
assigned to all human chromosomes, the pattern of the newly identified
placental protein population is proportional to that of the gene count
distribution of each chromosome. We also identified 219 unique <i>N</i>-linked glycopeptides, 592 unique phosphopeptides, and
66 chromosome 13-specific proteins. In particular, protein evidence
of 14 genes previously known to be specifically up-regulated in human
placenta was verified by mass spectrometry. With respect to the functional
implication of these proteins, 38 proteins were found to be involved
in regulatory factor biosynthesis or the immune system in the placenta,
but the molecular mechanism of these proteins during pregnancy warrants
further investigation. As far as we know, this work produced the highest
number of proteins identified in the placenta and will be useful for
annotating and mapping all proteins encoded in the human genome
Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project
As a starting point of the Chromosome-Centric Human Proteome
Project
(C-HPP), we established strategies of genome-wide proteomic analysis,
including protein identification, quantitation of disease-specific
proteins, and assessment of post-translational modifications, using
paired human placental tissues from healthy and preeclampsia patients.
This analysis resulted in identification of 4239 unique proteins with
high confidence (two or more unique peptides with a false discovery
rate less than 1%), covering 21% of approximately 20 059 (Ensembl
v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially
expressed preeclampsia-specific proteins. When these proteins are
assigned to all human chromosomes, the pattern of the newly identified
placental protein population is proportional to that of the gene count
distribution of each chromosome. We also identified 219 unique <i>N</i>-linked glycopeptides, 592 unique phosphopeptides, and
66 chromosome 13-specific proteins. In particular, protein evidence
of 14 genes previously known to be specifically up-regulated in human
placenta was verified by mass spectrometry. With respect to the functional
implication of these proteins, 38 proteins were found to be involved
in regulatory factor biosynthesis or the immune system in the placenta,
but the molecular mechanism of these proteins during pregnancy warrants
further investigation. As far as we know, this work produced the highest
number of proteins identified in the placenta and will be useful for
annotating and mapping all proteins encoded in the human genome
Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins
One
of the major goals of the Chromosome-Centric Human Proteome
Project (C-HPP) is to fill the knowledge gaps between human genomic
information and the corresponding proteomic information. These gaps
are due to “missing” proteins (MPs)predicted
proteins with insufficient evidence from mass spectrometry (MS), biochemical,
structural, or antibody analysesthat currently account for
2579 of the 19587 predicted human proteins (neXtProt, 2017-01).
We address some of the lessons learned from the inconsistent annotations
of missing proteins in databases (DB) and demonstrate a systematic
proteogenomic approach designed to explore a potential new function
of a known protein. To illustrate a cautious and strategic approach
for characterization of novel function in vitro and in vivo, we present
the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1;
hereafter NHERF1), which was mistakenly labeled as an MP in one DB
(Global Proteome Machine Database; GPMDB, 2011-09 release) but was
well known in another public DB and in the literature. As a first
step, NHERF1 was determined by MS and immunoblotting for its molecular
identity. We next investigated the potential new function of NHERF1
by carrying out the quantitative MS profiling of placental trophoblasts
(PXD004723) and functional study of cytotrophoblast JEG-3 cells. We
found that NHERF1 was associated with trophoblast differentiation
and motility. To validate this newly found cellular function of NHERF1,
we used the <i>Caenorhabditis elegans</i> mutant of <i>nrfl-1</i> (a nematode ortholog of <i>NHERF1</i>),
which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype,
and performed genetic complementation work. The <i>nrfl-1</i> mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human <i>NHERF1</i>. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future
Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins
One
of the major goals of the Chromosome-Centric Human Proteome
Project (C-HPP) is to fill the knowledge gaps between human genomic
information and the corresponding proteomic information. These gaps
are due to “missing” proteins (MPs)predicted
proteins with insufficient evidence from mass spectrometry (MS), biochemical,
structural, or antibody analysesthat currently account for
2579 of the 19587 predicted human proteins (neXtProt, 2017-01).
We address some of the lessons learned from the inconsistent annotations
of missing proteins in databases (DB) and demonstrate a systematic
proteogenomic approach designed to explore a potential new function
of a known protein. To illustrate a cautious and strategic approach
for characterization of novel function in vitro and in vivo, we present
the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1;
hereafter NHERF1), which was mistakenly labeled as an MP in one DB
(Global Proteome Machine Database; GPMDB, 2011-09 release) but was
well known in another public DB and in the literature. As a first
step, NHERF1 was determined by MS and immunoblotting for its molecular
identity. We next investigated the potential new function of NHERF1
by carrying out the quantitative MS profiling of placental trophoblasts
(PXD004723) and functional study of cytotrophoblast JEG-3 cells. We
found that NHERF1 was associated with trophoblast differentiation
and motility. To validate this newly found cellular function of NHERF1,
we used the <i>Caenorhabditis elegans</i> mutant of <i>nrfl-1</i> (a nematode ortholog of <i>NHERF1</i>),
which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype,
and performed genetic complementation work. The <i>nrfl-1</i> mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human <i>NHERF1</i>. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future
Standard Guidelines for the Chromosome-Centric Human Proteome Project
The objective of the international Chromosome-Centric
Human Proteome
Project (C-HPP) is to map and annotate all proteins encoded by the
genes on each human chromosome. The C-HPP consortium was established
to organize a collaborative network among the research teams responsible
for protein mapping of individual chromosomes and to identify compelling
biological and genetic mechanisms influencing colocated genes and
their protein products. The C-HPP aims to foster the development of
proteome analysis and integration of the findings from related molecular
-omics technology platforms through collaborations among universities,
industries, and private research groups. The C-HPP consortium leadership
has elicited broad input for standard guidelines to manage these international
efforts more efficiently by mobilizing existing resources and collaborative
networks. The C-HPP guidelines set out the collaborative consensus
of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency
of data, governance of the consortium, and collaborative benefits.
A companion approach for the Biology and Disease-Driven HPP (B/D-HPP)
component of the Human Proteome Project is currently being organized,
building upon the Human Proteome Organization's organ-based and biofluid-based
initiatives (www.hupo.org/research). The common application
of these guidelines in the participating laboratories is expected
to facilitate the goal of a comprehensive analysis of the human proteome