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Hu P, Luo S, Qu G, Luo Q, Tian Y, Huang K, Sun T. Identification and validation of feature genes associated with M1 macrophages in preeclampsia. Aging (Albany NY) 2023; 15:13822-13839. [PMID: 38048229 PMCID: PMC10756132 DOI: 10.18632/aging.205264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Preeclampsia (PE) is a pregnancy-specific cardiovascular complication that is the leading cause of maternal and neonatal morbidity and mortality. Previous studies have indicated the importance of immune cells, such as M1 and M2 macrophages, in the pathogenesis of PE. However, the mechanisms leading to immune dysregulation are unclear. Data-independent acquisition proteomic analysis was performed on placental tissues collected from patients with PE and healthy controls. Transcriptome data for placenta samples from patients with PE and their corresponding controls were obtained from the Gene Expression Omnibus database. Differential analysis of transcriptome and proteome data between PE and control groups was performed using R software. Immunocytic infiltration scoring was performed using the quantiseq algorithm. Weighted gene co-expression network analysis (WGCNA) screened for feature genes associated with M1 cell infiltration. Protein-protein interaction (PPI) analysis identified hub genes. We confirm that the infiltration score of M1 macrophages was significantly increased in the placental tissues of patients with PE. Differential analysis, WGCNA, and PPI analysis identified four hub molecules associated with M1 cell infiltration (HTRA4, POGK, MFAP5, and INHBA). The hub molecules displayed dysregulated expression in PE tissues. The qPCR, Western blots, and immunohistochemistry analyses confirmed that Inhibin, beta A (INHBA) was highly expressed in placental tissues of patients with PE. Immunofluorescence revealed the extensive infiltration of M1 macrophages in the placental tissues of patients with PE and their co-localization with INHBA. The collective results identified hub genes associated with M1 macrophage infiltration, providing potential targets for the pathogenesis and treatment of PE.
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Affiliation(s)
- Panpan Hu
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Shanshun Luo
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Guangjin Qu
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Qiqi Luo
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yu Tian
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Kun Huang
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Tingting Sun
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
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2
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Elkin ER, Su AL, Kilburn BA, Bakulski KM, Armant DR, Loch-Caruso R. Toxicity assessments of selected trichloroethylene and perchloroethylene metabolites in three in vitro human placental models. Reprod Toxicol 2022; 109:109-120. [PMID: 35304307 PMCID: PMC9107309 DOI: 10.1016/j.reprotox.2022.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 01/25/2023]
Abstract
Residential and occupational exposures to the industrial solvents perchloroethylene (PERC) and trichloroethylene (TCE) present public health concerns. In humans, maternal PERC and TCE exposures can be associated with adverse birth outcomes. Because PERC and TCE are biotransformed to toxic metabolites and placental dysfunction can contribute to adverse birth outcomes, the present study compared the toxicity of key PERC and TCE metabolites in three in vitro human placenta models. We measured cell viability and caspase 3 + 7 activity in the HTR-8/SVneo and BeWo cell lines, and caspase 3 + 7 activity in first trimester villous explant cultures. Cultures were exposed for 24 h to 5-100 µM S-(1,2-dichlorovinyl)-L-cysteine (DCVC) and S-(1,2,2-trichlorovinyl)-L-cysteine (TCVC), or 5-200 µM trichloroacetate (TCA) and dichloroacetate (DCA). DCVC significantly reduced cell viability and increased caspase 3 + 7 activity in HTR-8/SVneo cells at a lower concentration (20 µM) compared with concentrations toxic to BeWo cells and villous explants. Similarly, TCVC reduced cell viability and increased caspase 3 + 7 activity in HTR-8/SVneo cells but not in BeWo cells. TCA and DCA had only negligible effects on HTR-8/SVneo or BeWo cells. This study advances understanding of potential risks of PERC and TCE exposure during pregnancy by identifying metabolites toxic in placental cells and tissues.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA.
| | - Anthony L Su
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian A Kilburn
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - D Randall Armant
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA; Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
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3
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Na K, Kim M, Kim CY, Lim JS, Cho JY, Shin H, Lee HJ, Kang BJ, Han DH, Kim H, Baik JH, Swiatek-de Lange M, Karl J, Paik YK. Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth. J Proteome Res 2020; 19:4867-4883. [PMID: 33206527 DOI: 10.1021/acs.jproteome.0c00787] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We previously reported that human carboxylesterase 1 (CES1), a serine esterase containing a unique N-linked glycosyl group at Asn79 (N79 CES1), is a candidate serological marker of hepatocellular carcinoma (HCC). CES1 is normally present at low-to-undetectable levels in normal human plasma, HCC tumors, and major liver cancer cell lines. To investigate the potential mechanism underlying the suppression of CES1 expression in liver cancer cells, we took advantage of the low detectability of this marker in tumors by overexpressing CES1 in multiple HCC cell lines, including stable Hep3B cells. We found that the population of CES1-overexpressing (OE) cells decreased and that their doubling time was longer compared with mock control liver cancer cells. Using interactive transcriptome, proteome, and subsequent Gene Ontology enrichment analysis of CES1-OE cells, we found substantial decreases in the expression levels of genes involved in cell cycle regulation and proliferation. This antiproliferative function of the N79 glycan of CES1 was further supported by quantitative real-time polymerase chain reaction, flow cytometry, and an apoptosis protein array assay. An analysis of the levels of key signaling target proteins via Western blotting suggested that CES1 overexpression exerted an antiproliferative effect via the PKD1/PKCμ signaling pathway. Similar results were also seen in another HCC cell line (PLC/RFP/5) after transient transfection with CES1 but not in similarly treated non-HCC cell lines (e.g., HeLa and Tera-1 cells), suggesting that CES1 likely exerts a liver cell-type-specific suppressive effect. Given that the N-linked glycosyl group at Asn79 (N79 glycan) of CES1 is known to influence CES1 enzyme activity, we hypothesized that the post-translational modification of CES1 at N79 may be linked to its antiproliferative activity. To investigate the regulatory effect of the N79 glycan on cellular growth, we mutated the single N-glycosylation site in CES1 from Asn to Gln (CES1-N79Q) via site-directed mutagenesis. Fluorescence 2-D difference gel electrophoresis protein expression analysis of cell lysates revealed an increase in cell growth and a decrease in doubling time in cells carrying the N79Q mutation. Thus our results suggest that CES1 exerts an antiproliferative effect in liver cancer cells and that the single N-linked glycosylation at Asn79 plays a potential regulatory role. These functions may underlie the undetectability of CES1 in human HCC tumors and liver cancer cell lines. Mass spectrometry data are available via ProteomeXchange under the identifier PXD021573.
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Affiliation(s)
- Keun Na
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Minjoo Kim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Heon Shin
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Hyo Jin Lee
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | - Byeong Jun Kang
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | | | | | - Ja-Hyun Baik
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | | | - Johann Karl
- Roche Diagnostics, GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
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4
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Elkin ER, Bridges D, Harris SM, Loch-Caruso RK. Exposure to Trichloroethylene Metabolite S-(1,2-Dichlorovinyl)-L-cysteine Causes Compensatory Changes to Macronutrient Utilization and Energy Metabolism in Placental HTR-8/SVneo Cells. Chem Res Toxicol 2020; 33:1339-1355. [PMID: 31951115 PMCID: PMC7299793 DOI: 10.1021/acs.chemrestox.9b00356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Trichloroethylene
(TCE) is a widespread environmental contaminant
following decades of use as an industrial solvent, improper disposal,
and remediation challenges. Consequently, TCE exposure continues to
constitute a risk to human health. Despite epidemiological evidence
associating exposure with adverse birth outcomes, the effects of TCE
and its metabolite S-(1, 2-dichlorovinyl)-L-cysteine
(DCVC) on the placenta remain undetermined. Flexible and efficient
macronutrient and energy metabolism pathway utilization is essential
for placental cell physiological adaptability. Because DCVC is known
to compromise cellular energy status and disrupt energy metabolism
in renal proximal tubular cells, this study investigated the effects
of DCVC on cellular energy status and energy metabolism pathways in
placental cells. Human extravillous trophoblast cells, HTR-8/SVneo,
were exposed to 5–20 μM DCVC for 6 or 12 h. After establishing
concentration and exposure duration thresholds for DCVC-induced cytotoxicity,
targeted metabolomics was used to evaluate overall energy status and
metabolite concentrations from energy metabolism pathways. The data
revealed glucose metabolism perturbations including a time-dependent
accumulation of glucose-6-phosphate+frutose-6-phosphate (G6P+F6P)
as well as independent shunting of glucose intermediates that diminished
with time, with modest energy status decline but in the absence of
significant changes in ATP concentrations. Furthermore, metabolic
profiling suggested that DCVC stimulated compensatory utilization
of glycerol, lipid, and amino acid metabolism to provide intermediate
substrates entering downstream in the glycolytic pathway or the tricarboxylic
acid cycle. Lastly, amino acid deprivation increased susceptibility
to DCVC-induced cytotoxicity. Taken together, these results suggest
that DCVC caused metabolic perturbations necessitating adaptations
in macronutrient and energy metabolism pathway utilization to maintain
adequate ATP levels.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Sean M Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Rita Karen Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
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5
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Elkin ER, Bridges D, Loch-Caruso R. The trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine induces progressive mitochondrial dysfunction in HTR-8/SVneo trophoblasts. Toxicology 2019; 427:152283. [PMID: 31476333 DOI: 10.1016/j.tox.2019.152283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 02/08/2023]
Abstract
Trichloroethylene is an industrial solvent and common environmental pollutant. Despite efforts to ban trichloroethylene, its availability and usage persist globally, constituting a hazard to human health. Recent studies reported associations between maternal trichloroethylene exposure and increased risk for low birth weight. Despite these associations, the toxicological mechanism underlying trichloroethylene adverse effects on pregnancy remains largely unknown. The trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) induces mitochondrial-mediated apoptosis in a trophoblast cell line. To gain further understanding of mitochondrial-mediated DCVC placental toxicity, this study investigated the effects of DCVC exposure on mitochondrial function using non-cytolethal concentrations in placental cells. Human trophoblasts, HTR-8/SVneo, were exposed in vitro to a maximum of 20 μM DCVC for up to 12 h. Cell-based oxygen consumption and extracellular acidification assays were used to evaluate key aspects of mitochondrial function. Following 6 h of exposure to 20 μM DCVC, elevated oxygen consumption, mitochondrial proton leak and sustained energy coupling deficiency were observed. Similarly, 12 h of exposure to 20 μM DCVC decreased mitochondrial-dependent basal, ATP-linked and maximum oxygen consumption rates. Using the fluorochrome TMRE, dissipation of mitochondrial membrane potential was detected after a 12-h exposure to 20 μM DCVC, and (±)-α-tocopherol, a known suppressor of lipid peroxidation, attenuated DCVC-stimulated mitochondrial membrane depolarization but failed to rescue oxygen consumption perturbations. Together, these results suggest that DCVC caused progressive mitochondrial dysfunction, resulting in lipid peroxidation-associated mitochondrial membrane depolarization. Our findings contribute to the biological plausibility of DCVC-induced placental impairment and provide new insights into the role of the mitochondria in DCVC-induced toxicity.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.
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6
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Abdulghani M, Song G, Kaur H, Walley JW, Tuteja G. Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. J Proteome Res 2019; 18:2088-2099. [PMID: 30986076 DOI: 10.1021/acs.jproteome.8b00970] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The condition of the placenta is a determinant of the short- and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multiomics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental time points. We found that incorporating information from both the transcriptome and proteome identifies genes associated with time point-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated on the basis of the proteome data but not the transcriptome data at each time point, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome data set, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome data sets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.
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Affiliation(s)
- Majd Abdulghani
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Haninder Kaur
- Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Justin W Walley
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Geetu Tuteja
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
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7
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Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2). PLoS Negl Trop Dis 2018; 12:e0006351. [PMID: 29608573 PMCID: PMC5897034 DOI: 10.1371/journal.pntd.0006351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 04/12/2018] [Accepted: 02/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2. Methods/Principal findings The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms. Conclusions and significance This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method allows T. cruzi strain typing using MS/MS spectra as discriminatory features and allows the differentiation of TcI-TcVI DTUs. Similar to genomic-based strategies, the Tc-STAMS2 method allows identification of strains within DTUs. Its robustness towards different experimental and biological variables makes it a valuable complementary strategy to the current T. cruzi genotyping assays. Moreover, this method can be used to identify DTU-specific features correlated with the strain phenotype. Chagas disease is one of the most important neglected diseases with an estimated number of 6–7 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically diverse and a new nomenclature assigned each strain to seven genetic groups (TcI-TcVI and Tcbat), named Discrete Typing Units (DTUs), based on their biochemical, immunological and phenotypical characteristics. T.cruzi DTUs have been correlated to diverse clinical outcomes highlighting the importance of molecular epidemiological screens. Despite the development of T.cruzi typing methods based on genetic signatures, each method presents its own advantages and challenges. The work presented here shows the application of mass spectrometry for Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2). The novelty of the method is based on the use of peptide fragmentation spectra as strain-specific fingerprints to classify and identify DTUs. Initially, a spectra library is generated from characterized T.cruzi strains. The library is subsequently inspected using MS/MS spectra from unknown strains and confidently assigned to a specific strain in an automated and computationally-driven approach. The Tc-STAMS2 method was challenged to test several variables such as sample type and preparation, instrument setup and identification platform. Tc-STAMS2 provided high confidence and robustness in T.cruzi strain typing. The Tc-STAMS2 method represents a proof-of-concept of a complementary strategy to the current DNA-based T. cruzi genotyping methods. Moreover, the method allows the identification of strain-specific features that could be related to the biology of T.cruzi strains and their clinical outcomes.
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8
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Ohmaru-Nakanishi T, Asanoma K, Fujikawa M, Fujita Y, Yagi H, Onoyama I, Hidaka N, Sonoda K, Kato K. Fibrosis in Preeclamptic Placentas Is Associated with Stromal Fibroblasts Activated by the Transforming Growth Factor-β1 Signaling Pathway. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:683-695. [DOI: 10.1016/j.ajpath.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/12/2017] [Accepted: 11/02/2017] [Indexed: 01/11/2023]
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9
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Na K, Shin H, Cho JY, Jung SH, Lim J, Lim JS, Kim EA, Kim HS, Kang AR, Kim JH, Shin JM, Jeong SK, Kim CY, Park JY, Chung HM, Omenn GS, Hancock WS, Paik YK. Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins. J Proteome Res 2017; 16:4455-4467. [PMID: 28960081 DOI: 10.1021/acs.jproteome.7b00146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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 analyses-that 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 Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. 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.
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Affiliation(s)
- Keun Na
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, South Korea
| | - Heon Shin
- Department of Integrated OMICS for Biomedical Science, Yonsei University , Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, South Korea
| | - Sang Hee Jung
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University , Seongnam 13496, South Korea
| | - Jaeseung Lim
- CHA Biotech Co., Ltd. , Seongnam 13488, South Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, South Korea
| | - Eun Ah Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University , Seongnam 13496, South Korea
| | - Hye Sun Kim
- CHA Biotech Co., Ltd. , Seongnam 13488, South Korea
| | - Ah Reum Kang
- CHA Biotech Co., Ltd. , Seongnam 13488, South Korea
| | - Ji Hye Kim
- CHA Biotech Co., Ltd. , Seongnam 13488, South Korea
| | - Jeong Min Shin
- Department of Biochemistry, CHA University , Seongnam 13488, South Korea
| | - Seul-Ki Jeong
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, South Korea
| | - Chae-Yeon Kim
- Department of Integrated OMICS for Biomedical Science, Yonsei University , Seoul 03722, South Korea
| | - Jun Young Park
- Department of Integrated OMICS for Biomedical Science, Yonsei University , Seoul 03722, South Korea
| | - Hyung-Min Chung
- Department of Medicine, School of Medicine, Konkuk University , Seoul 143701, South Korea
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - William S Hancock
- Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 03722, South Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University , Seoul 03722, South Korea.,Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul 03722, South Korea
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10
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Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P. Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J Proteome Res 2017; 16:4352-4363. [PMID: 28959888 DOI: 10.1021/acs.jproteome.7b00340] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin. Therefore, a multiprotease strategy was used for searching more MPs in the same human testis tissues separated by 10% SDS-PAGE, followed by high resolution LC-MS/MS system (Q Exactive HF). A total of 7838 proteins were identified. Among them, three PE2 MPs in neXtProt 2017-01 have been identified: beta-defensin 123 ( Q8N688 , chr 20q), cancer/testis antigen family 45 member A10 ( P0DMU9 , chr Xq), and Histone H2A-Bbd type 2/3 ( P0C5Z0 , chr Xq). However, because only one unique peptide of ≥9 AA was identified in beta-defensin 123 and Histone H2A-Bbd type 2/3, respectively, further analysis indicates that each falls under the exceptions clause of the HPP Guidelines v2.1. After a spectrum quality check, isobaric PTM and single amino acid variant (SAAV) filtering, and verification with a synthesized peptide, and based on overlapping peptides from different proteases, these three MPs should be considered as exemplary examples of MPs found by exceptional criteria. Other MPs were considered as candidates but need further validation. All MS data sets have been deposited to the ProteomeXchange with identifier PXD006465.
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Affiliation(s)
- Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Yang Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University , Guangzhou 510275, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yue Gao
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China.,Graduate School, Anhui Medical University , Hefei 230032, China.,Tianjin Baodi Hospital , Tianjin 301800, China
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11
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Hernández-Díaz N, Torres R, Ramírez-Pinilla MP. Proteomic Profile of Mabuya sp. (Squamata: Scincidae) Ovary and Placenta During Gestation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:371-389. [PMID: 28397398 DOI: 10.1002/jez.b.22739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 02/07/2023]
Abstract
Reptiles are one of the most diverse groups of vertebrates, providing an integrated system for comparative studies on metabolic, animal physiology, and developmental biology. However, the molecular data available are limited and only recently have started to call attention in the "omics" sciences. Mabuya sp. is a viviparous placentrotrophic skink with particular reproductive features, including microlecithal eggs, early luteolysis, prolonged gestation, and development of a highly specialized placenta. This placenta is responsible for respiratory exchange and the transference of all nutrients necessary for embryonic development. Our aim was to identify differentially expressed proteins in the ovary and placenta of Mabuya sp. during early, mid, and late gestation; their possible metabolic pathways; and biological processes. We carried out a comparative proteomic analysis during gestation in both tissues by sodium dodecyl sulfate polyacrylamide gel electrophoresis, two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization. Differential protein expression in both tissues (Student's t-test P < 0.05) was related to several processes such as cell structure, cell movement, and energy. Proteins found in ovary are mainly associated with follicular development and its regulation. In the placenta, particularly during mid and late gestation, protein expression is involved in nutrient metabolism, transport, protein synthesis, and embryonic development. This work provides new insights about the proteins expressed and their physiological mechanisms in Mabuya sp. placenta and ovary during gestation.
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Affiliation(s)
- Nathaly Hernández-Díaz
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia.,Grupo de Investigación en Bioquímica y Microbiología, GIBIM, Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Rodrigo Torres
- Grupo de Investigación en Bioquímica y Microbiología, GIBIM, Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia.,Laboratorio de Biotecnología-CEO, Instituto Colombiano del Petróleo, ECOPETROL, Piedecuesta, Santander, Colombia
| | - Martha Patricia Ramírez-Pinilla
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
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12
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Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V. Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. J Proteome Res 2016; 15:4101-4115. [PMID: 27581094 PMCID: PMC5099979 DOI: 10.1021/acs.jproteome.6b00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
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.
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Affiliation(s)
- Alba Garin-Muga
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Leticia Odriozola
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain
| | - Ana Martínez-Val
- Proteomics Unit, Spanish National Cancer Research Centre , 28029, Madrid, Spain
| | - Noemí Del Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K
| | - Rocío Martínez
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Manuela Molina
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Laura Cantero
- Proteomics Unit (SCSIE), University of Valencia , 46010, Valencia, Spain
| | - Rocío Rivera
- Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain
| | - Nicolás Garrido
- Andrology Laboratory and Sperm Bank, Instituto Universitario IVI , 46015, Valencia, Spain
| | | | | | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust GenomeCampus, Hinxton, Cambridge, CB10 1SD, U.K
| | - Fernando J Corrales
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain.,Division of Hepatology and Gene Therapy, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain
| | - Victor Segura
- Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , 31008, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research , 31008, Pamplona, Spain
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13
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Rezadoost H, Karimi M, Jafari M. Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study. Sci Rep 2016; 6:30133. [PMID: 27452083 PMCID: PMC4959000 DOI: 10.1038/srep30133] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/24/2016] [Indexed: 12/24/2022] Open
Abstract
Lack of molecular biology evidence has led clinical success of alternative and complementary medicine (CAM) to be marginalized. In turn, a large portion of life Science researchers could not communicate and help to develop therapeutic potential laid in these therapeutic approaches. In this study, we began to quantify descriptive classification theory in one of the CAM branches i.e. Iranian traditional medicine (ITM). Using proteomic tools and network analysis, the expressed proteins and their relationships were studied in mitochondrial lysate isolated from PBMCs from two different temperaments i.e. Hot-wet (HW) and Cold-dry (CD). The 82% of the identified proteins are over- or under-represented in distinct temperaments. Also, our result showed the different protein-protein interaction networks (PPIN) represented in these two temperaments using centrality and module finding analysis. Following the gene ontology and pathway enrichment analysis, we have found enriched biological terms in each group which are in conformity with the physiologically known evidence in ITM. In conclusion, we argued that the network biology which naturally consider life at the system level along with the different omics data will pave the way toward explicit delineation of the CAM activities.
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Affiliation(s)
- Hassan Rezadoost
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mehrdad Karimi
- Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran.,School of Traditional Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 131694-3551, Iran
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14
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Huuskonen P, Amezaga MR, Bellingham M, Jones LH, Storvik M, Häkkinen M, Keski-Nisula L, Heinonen S, O'Shaughnessy PJ, Fowler PA, Pasanen M. The human placental proteome is affected by maternal smoking. Reprod Toxicol 2016; 63:22-31. [PMID: 27189315 PMCID: PMC4991937 DOI: 10.1016/j.reprotox.2016.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/29/2016] [Accepted: 05/13/2016] [Indexed: 11/23/2022]
Abstract
The effects of maternal smoking on the term placental proteome was studied. Maternal smoking significantly affected 18% of protein spots. Maternal smoking affects systems controlling the development and function of placenta. The observed placental changes may contribute to the lowered birth weights.
Detrimental effects of maternal smoking on the term placental proteome and steroid-metabolizing activities, and maternal hormone levels, were studied by using seven non-smoker and seven smoker placentae. Smoking significantly affected 18% of protein spots. The functional networks affected were i) cell morphology, cellular assembly and organization, cellular compromise (15 hits) and ii) DNA replication, recombination, and repair, energy production, nucleic acid metabolism (6 hits). Smoking significantly up-regulated such proteins as, SERPINA1, EFHD1 and KRT8; and down-regulated SERPINB2, FGA and HBB. Although maternal plasma steroids were not significantly altered, the catalytic activity of CYP1A1 was increased whereas CYP19A1 activity was reduced by smoking. Furthermore, transcript expression of CYP1A1 and CYP4B1 were induced while HSD17B2, NFKB and TGFB1 were repressed by smoking. The observed smoking induced wide-spread changes on placental proteome and transcript levels may contribute to the lowered birth weights of the new-born child and placenta.
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Affiliation(s)
- Pasi Huuskonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, FIN-70211, Kuopio, Finland
| | - Maria R Amezaga
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Michelle Bellingham
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Lucy H Jones
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Markus Storvik
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, FIN-70211, Kuopio, Finland
| | - Merja Häkkinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, FIN-70211, Kuopio, Finland
| | - Leea Keski-Nisula
- Department of Obstetrics and Gynaecology, Kuopio University Hospital, FIN-70211 Kuopio, Finland
| | - Seppo Heinonen
- Department of Obstetrics and Gynaecology, Kuopio University Hospital, FIN-70211 Kuopio, Finland
| | - Peter J O'Shaughnessy
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Paul A Fowler
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Markku Pasanen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, FIN-70211, Kuopio, Finland.
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15
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Kim S, Lee HJ, Hahm JH, Jeong SK, Park DH, Hancock WS, Paik YK. Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans. J Proteome Res 2016; 15:531-9. [DOI: 10.1021/acs.jproteome.5b00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunhee Kim
- Department
of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Hyoung-Joo Lee
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Jeong-Hoon Hahm
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Seul-Ki Jeong
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Don-Ha Park
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - William S. Hancock
- Department
of Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States,
| | - Young-Ki Paik
- Department
of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
- Department
of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
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16
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Cho JY, Lee HJ, Jeong SK, Kim KY, Kwon KH, Yoo JS, Omenn GS, Baker MS, Hancock WS, Paik YK. Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:4959-66. [DOI: 10.1021/acs.jproteome.5b00578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jin-Young Cho
- Yonsei
Proteome Research Center, Department of Integrated OMICS for Biomedical
Science and Department of Biochemistry, College of Life Science and
Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemoon-gu, Seoul 120-749, Korea
| | - Hyoung-Joo Lee
- Yonsei
Proteome Research Center, Department of Integrated OMICS for Biomedical
Science and Department of Biochemistry, College of Life Science and
Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemoon-gu, Seoul 120-749, Korea
| | - Seul-Ki Jeong
- Yonsei
Proteome Research Center, Department of Integrated OMICS for Biomedical
Science and Department of Biochemistry, College of Life Science and
Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemoon-gu, Seoul 120-749, Korea
| | - Kwang-Youl Kim
- Yonsei
Proteome Research Center, Department of Integrated OMICS for Biomedical
Science and Department of Biochemistry, College of Life Science and
Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemoon-gu, Seoul 120-749, Korea
| | | | | | - Gilbert S. Omenn
- Center
for Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor 48109, Michigan United States
| | - Mark S. Baker
- Department
of Biomedical Science, Faculty of Medicine and Health Science, Macquarie University, New South Wales 2109, Australia
| | | | - Young-Ki Paik
- Yonsei
Proteome Research Center, Department of Integrated OMICS for Biomedical
Science and Department of Biochemistry, College of Life Science and
Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemoon-gu, Seoul 120-749, Korea
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17
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Jeong SK, Hancock WS, Paik YK. GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3710-9. [PMID: 26272709 DOI: 10.1021/acs.jproteome.5b00541] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.
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Affiliation(s)
- Seul-Ki Jeong
- Yonsei Proteome Research Center and Biomedical Proteome Research Center , 50 Yonsei-Ro, Seodaemun-gu, Seoul 120-749, Korea
| | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 12 Oxford Street, Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center and Biomedical Proteome Research Center , 50 Yonsei-Ro, Seodaemun-gu, Seoul 120-749, Korea.,Department of Biochemistry, Department of Integrated Omics for Biomedical Science (World Class University Graduate Program), Yonsei University , 50 Yonsei-Ro, Sudaemoon-ku, Seoul 120-749, Korea
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18
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Zhang Y, Li Q, Wu F, Zhou R, Qi Y, Su N, Chen L, Xu S, Jiang T, Zhang C, Cheng G, Chen X, Kong D, Wang Y, Zhang T, Zi J, Wei W, Gao Y, Zhen B, Xiong Z, Wu S, Yang P, Wang Q, Wen B, He F, Xu P, Liu S. Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins. J Proteome Res 2015; 14:3583-94. [DOI: 10.1021/acs.jproteome.5b00435] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yao Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qidan Li
- CAS
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- BGI-Shenzhen, Shenzhen 518083, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Feilin Wu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Life Science
College, Southwest Forestry University, Kunming 650224, P. R, China
| | - Ruo Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yingzi Qi
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Na Su
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Lingsheng Chen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | | | - Tao Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chengpu Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | | | - Xinguo Chen
- Institute of Organ Transportation, General Hospital of Chinese People’s Armed Police Forces, Beijing 100039, China
| | - Degang Kong
- General
Surgery Dept., Capital Medical University Affiliated Beijing YouAn Hospital, Beijing 100069, China
| | | | - Tao Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Wei
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yuan Gao
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Bei Zhen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Zhi Xiong
- Life Science
College, Southwest Forestry University, Kunming 650224, P. R, China
| | - Songfeng Wu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Pengyuan Yang
- Institutes
of Biomedical Sciences, Department of Chemistry and Zhongshan Hospital, Fudan University, 130 DongAn Road, Shanghai 200032, China
| | - Quanhui Wang
- CAS
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- BGI-Shenzhen, Shenzhen 518083, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fuchu He
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ping Xu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Siqi Liu
- CAS
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- BGI-Shenzhen, Shenzhen 518083, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
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19
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Su N, Zhang C, Zhang Y, Wang Z, Fan F, Zhao M, Wu F, Gao Y, Li Y, Chen L, Tian M, Zhang T, Wen B, Sensang N, Xiong Z, Wu S, Liu S, Yang P, Zhen B, Zhu Y, He F, Xu P. Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples. J Proteome Res 2015; 14:3680-92. [DOI: 10.1021/acs.jproteome.5b00481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Na Su
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Chengpu Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yao Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute
of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Zhiqiang Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education , and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Fengxu Fan
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Anhui Medical University, Hefei 230032, Anhui China
| | - Mingzhi Zhao
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Feilin Wu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Life
Science College, Southwest Forestry University, Kunming 650224, China
| | - Yuan Gao
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yanchang Li
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Lingsheng Chen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- State Key
Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Miaomiao Tian
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Tao Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Bo Wen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Na Sensang
- Inner Mongolia Medical University, Hohhot 010110, Inner Mongolia China
| | - Zhi Xiong
- Life
Science College, Southwest Forestry University, Kunming 650224, China
| | - Songfeng Wu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Pengyuan Yang
- Institute
of Biomedical Sciences, Department of Chemistry, and Zhongshan Hospital, Fudan University, 130 DongAn Road, Shanghai 200032, China
| | - Bei Zhen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yunping Zhu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Fuchu He
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ping Xu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education , and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Anhui Medical University, Hefei 230032, Anhui China
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20
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Park M, Lim JS, Lee HJ, Na K, Lee MJ, Kang CM, Paik YK, Kim H. Distinct Protein Expression Profiles of Solid-Pseudopapillary Neoplasms of the Pancreas. J Proteome Res 2015; 14:3007-14. [PMID: 26148796 DOI: 10.1021/acs.jproteome.5b00423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Solid-pseudopapillary neoplasm (SPN) is an uncommon pancreatic tumor with mutation in CTNNB1 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.
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Affiliation(s)
| | - Jong-Sun Lim
- §Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul 120-749, Korea
| | - Hyoung-Joo Lee
- §Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul 120-749, Korea
| | - Keun Na
- §Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul 120-749, Korea
| | - Min Jung Lee
- §Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul 120-749, Korea
| | | | - Young-Ki Paik
- §Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul 120-749, Korea
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21
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Lee DG, Nam J, Kim SW, Kang YM, An HJ, Kim CW, Choi JS. Proteomic analysis of reproduction proteins involved in litter size from porcine placenta. Biosci Biotechnol Biochem 2015; 79:1414-21. [PMID: 25921448 DOI: 10.1080/09168451.2015.1039478] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography-tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.
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Affiliation(s)
- Dong-Gi Lee
- a Biological Disaster Analysis Group , Korea Basic Science Institute , Daejeon , Republic of Korea
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22
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Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet 2014; 23:5866-78. [PMID: 24939910 PMCID: PMC4204768 DOI: 10.1093/hmg/ddu309] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort.
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Affiliation(s)
| | - David Juan
- Structural Biology and Bioinformatics Programme and
| | - Jose Manuel Rodriguez
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Jesus Vazquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme and, National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain,
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23
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Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LDN, Balakrishnan L, Subbannayya T, Yan F, Prasad TSK, Gowda H, Lee C, Hancock WS, Pandey A. Functional annotation of proteome encoded by human chromosome 22. J Proteome Res 2014; 13:2749-60. [PMID: 24669763 PMCID: PMC4059257 DOI: 10.1021/pr401169d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As
part of the chromosome-centric human proteome project (C-HPP)
initiative, we report our progress on the annotation of chromosome 22.
Chromosome 22, spanning 51 million base pairs, was the first chromosome
to be sequenced. Gene dosage alterations on this chromosome have been
shown to be associated with a number of congenital anomalies. In addition,
several rare but aggressive tumors have been associated with this
chromosome. A number of important gene families including immunoglobulin
lambda locus, Crystallin beta family, and APOBEC gene family are located
on this chromosome. On the basis of proteomic profiling of 30 histologically
normal tissues and cells using high-resolution mass spectrometry,
we show protein evidence of 367 genes on chromosome 22. Importantly,
this includes 47 proteins, which are currently annotated as “missing”
proteins. We also confirmed the translation start sites of 120 chromosome 22-encoded
proteins. Employing a comprehensive proteogenomics analysis pipeline,
we provide evidence of novel coding regions on this chromosome which
include upstream ORFs and novel exons in addition to correcting existing
gene structures. We describe tissue-wise expression of the proteins
and the distribution of gene families on this chromosome. These data
have been deposited to ProteomeXchange with the identifier PXD000561.
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Affiliation(s)
- Sneha M Pinto
- Institute of Bioinformatics, International Tech Park , Bangalore, Karnataka 560066, India
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24
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Lee HJ, Cha HJ, Lim JS, Lee SH, Song SY, Kim H, Hancock WS, Yoo JS, Paik YK. Abundance-ratio-based semiquantitative analysis of site-specific N-linked glycopeptides present in the plasma of hepatocellular carcinoma patients. J Proteome Res 2014; 13:2328-38. [PMID: 24628331 DOI: 10.1021/pr4011519] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aberrant structures of site-specific N-linked glycans are closely associated with the tumorigenesis of hepatocellular carcinoma (HCC), one of the most common fatal cancers worldwide. Vitronectin (VTN) is considered a candidate glycobiomarker of HCC. In this study, we describe a reliable and simple quantification strategy based on abundance ratios of site-specific N-linked glycopeptides of VTN to screen for potential biomarkers. A total of 14 unique N-linked glycans corresponding to 27 unique N-linked glycopeptides were characterized at three N-linked sites (Asn-86, -169, and -242) present in VTN. These glycans could be good candidate markers for HCC. Among these glycans, the abundance ratio of two representative glycoforms (fucosyl vs non-fucosyl) was significantly increased in HCC plasma relative to normal plasma. This strategy was also successfully applied to another potential HCC biomarker, haptoglobin. Furthermore, we demonstrate that our approach employing tandem mass tag (TMT) and target N-linked glycopeptides of VTN is a useful tool for quantifying specific glycans in HCC plasma relative to normal plasma. Our strategy represents a simple and potentially useful screening platform for the discovery of cancer-specific glycobiomarkers.
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Affiliation(s)
- Hyoung-Joo Lee
- Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea
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25
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Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res 2013; 13:15-20. [PMID: 24364385 DOI: 10.1021/pr401144x] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One year ago the Human Proteome Project (HPP) leadership designated the baseline metrics for the Human Proteome Project to be based on neXtProt with a total of 13,664 proteins validated at protein evidence level 1 (PE1) by mass spectrometry, antibody-capture, Edman sequencing, or 3D structures. Corresponding chromosome-specific data were provided from PeptideAtlas, GPMdb, and Human Protein Atlas. This year, the neXtProt total is 15,646 and the other resources, which are inputs to neXtProt, have high-quality identifications and additional annotations for 14,012 in PeptideAtlas, 14,869 in GPMdb, and 10,976 in HPA. We propose to remove 638 genes from the denominator that are "uncertain" or "dubious" in Ensembl, UniProt/SwissProt, and neXtProt. That leaves 3844 "missing proteins", currently having no or inadequate documentation, to be found from a new denominator of 19,490 protein-coding genes. We present those tabulations and web links and discuss current strategies to find the missing proteins.
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Affiliation(s)
- Lydie Lane
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
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26
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Paik YK, Omenn GS, Thongboonkerd V, Marko-Varga G, Hancock WS. Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J Proteome Res 2013; 13:1-4. [PMID: 24328071 DOI: 10.1021/pr4011958] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Departments of Integrated Omics for Biomedical Science and Biochemistry, Yonsei University , 50 Yonsei-ro, Sudaemoon-ku, Seoul 120-749, Korea
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27
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Zhong J, Cui Y, Guo J, Chen Z, Yang L, He QY, Zhang G, Wang T. Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J Proteome Res 2013; 13:50-9. [PMID: 24200226 DOI: 10.1021/pr4007409] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of protein expression, quantification, and modification. We previously found that the analysis of translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance. Therefore, we propose here to use full-length RNC-mRNA information to illustrate protein expression both qualitatively and quantitatively. We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12,758 and 14,113 translating genes in human normal bronchial epithelial (HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively. We found that most of these genes were mapped with >80% of coding sequence coverage. In Caco-2 cells, we provided translating evidence on 4180 significant single-nucleotide variations. While using RNC-mRNA data as a standard for proteomic data integration, both translating and protein evidence of 7876 genes can be acquired from four interlaboratory data sets with different MS platforms. In addition, we detected 1397 noncoding mRNAs that were attached to ribosomes, suggesting a potential source of new protein explorations. By comparing the two cell lines, a total of 677 differentially translated genes were found to be nonevenly distributed across chromosomes. In addition, 2105 genes in Caco-2 and 750 genes in HBE cells are expressed in a cell-specific manner. These genes are significantly and specifically clustered on multiple chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations can be considerably improved by integrating RNC-mRNA analysis with MS, bioinformatics, and antibody-based verifications.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou 510632, China
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28
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Omenn GS. Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:866-73. [PMID: 24211518 DOI: 10.1016/j.bbapap.2013.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/17/2013] [Accepted: 10/31/2013] [Indexed: 12/24/2022]
Abstract
This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, MI, USA; Institute for Systems Biology, Seattle, WA, USA
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29
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Wang F, Shi Z, Wang P, You W, Liang G. Comparative proteome profile of human placenta from normal and preeclamptic pregnancies. PLoS One 2013; 8:e78025. [PMID: 24205073 PMCID: PMC3799759 DOI: 10.1371/journal.pone.0078025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
To better understand the molecular mechanisms involved in pathological development of placenta in preeclampsia, we used LC-MS/MS to construct a large-scale comparative proteome profile of human placentas from normal and preeclamptic pregnancies. A total of 2636 proteins were detected in human placentas, and 171 different proteins were definitively identified between control and preeclamptic placentas. Further bioinformatics analysis indicated that these differentially expressed proteins correlate with several specific cellular processes which occur during pathological changes of preeclamptic placenta. 6 proteins were randomly selected to verify their expression patterns with Western blotting. Of which, 3 proteins’ cellular localizations were validated with immunohistochemistry. Elucidation of how protein-expression changes coordinate the pathological development would provide researchers with a better understanding of the critical biological processes of preeclampsia and potential targets for therapeutic agents to regulate placenta function, and eventually benefit the treatment of preeclampsia.
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Affiliation(s)
- Fuqiang Wang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
- State Key Laboratory of Reproductive Medicine, Analysis Center, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhonghua Shi
- State Key Laboratory of Reproductive Medicine, Analysis Center, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ping Wang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China;
| | - Wei You
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China;
- * E-mails: (GL); (WY)
| | - Gaolin Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
- * E-mails: (GL); (WY)
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