Altered protein expression at early-stage rat hepatic neoplasia

2007 ◽  
Vol 292 (5) ◽  
pp. G1272-G1282 ◽  
Author(s):  
Qilie Luo ◽  
Linda Siconolfi-Baez ◽  
Pallavi Annamaneni ◽  
Mark T. Bielawski ◽  
Phyllis M. Novikoff ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Immunofluorescence Microscopy ◽  
Early Stage ◽  
Expression Patterns ◽  
Polyacrylamide Gel Electrophoresis ◽  
Normal Liver ◽  
Angiogenesis Inhibitors ◽  
Peptide Mass ◽  
Hepatic Neoplasia

Protein expression patterns were analyzed in a rat model of hepatic neoplasia to detect changes reflecting biological mechanism or potential therapeutic targets. The rat resistant hepatocyte model of carcinogenesis was studied, with a focus on the earliest preneoplastic lesion visible in the liver, the preneoplastic hyperplastic nodule. Expression differences were shown by two-dimensional polyacrylamide gel electrophoresis and image analysis. Polypeptide masses were measured by peptide mass fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) and their sequences were obtained by tandem mass spectrometry. Alterations in expression of cytoskeletal and functional proteins were demonstrated, consistent with biological changes known to occur in the preneoplastic cells. Of particular interest was the differential expression of a serine protease inhibitor (serpin) with a role implicated in angiogenesis. Serpin, implicated in the inhibition of angiogenesis, is present in normal liver but has greatly reduced expression at the preneoplastic stage of liver cancer development. Immunofluorescence microscopy with antibodies to this serpin, kallistatin, supports the proteomic identification. Immunofluorescence microscopy with antibodies to the blood vessel marker von Willebrand factor provides evidence for neovascularization in the liver containing multiple preneoplastic nodules. These observations suggest that at an early stage of liver carcinogenesis reduction or loss of angiogenesis inhibitors may contribute to initiation of neoangiogenesis. A number of other identified proteins known to be associated with hepatomas are also present at early-stage neoplasia.

scholarly journals Independent Validation of Candidate Breast Cancer Serum Biomarkers Identified by Mass Spectrometry

2005 ◽  
Vol 51 (12) ◽  
pp. 2229-2235 ◽  
Author(s):  
Jinong Li ◽  
Rosaria Orlandi ◽  
C Nicole White ◽  
Jason Rosenzweig ◽  
Jing Zhao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mass Spectrometry ◽  
Protein Expression ◽  
Expression Profiling ◽  
Protein Identification ◽  
Expression Patterns ◽  
Peptide Sequencing ◽  
Serum Samples ◽  
Peptide Mass ◽  
Sample Set

Abstract Background: We previously selected a panel of 3 breast cancer biomarkers (BC1, BC2, and BC3) from serum samples collected at a single hospital based on their collective contribution to the optimal separation of breast cancer patients and noncancer controls by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). The identities and general applicability of these markers, however, were unknown. In this study, we performed protein expression profiling on samples obtained from a second hospital, included a greater number of ductal carcinoma in situ (DCIS) cases, and performed purification and identification of the 2 confirmed markers. Methods: Using a case–control study design, we performed protein expression profiling on serum samples from the National Cancer Institute (Milan, Italy). The validation sample cohort consisted of 61 women with locally invasive breast cancer, 32 with DCIS, 37 with various benign breast diseases (including 13 atypical), and 46 age-matched apparently healthy women (age range, 44–68 years). Validated biomarkers were purified and identified with serial chromatography, 1-dimensional gel electrophoresis, in-gel ASP-N digestion, peptide mass fingerprinting, and tandem mass peptide sequencing. Results: The BC3 and BC2 expression patterns in this sample set were consistent with the first study sample set. BC3 and BC2 were identified to be complement component C3adesArg and a C-terminal–truncated form of C3adesArg, respectively. Conclusions: Evaluation of biomarkers in independent sample sets can help determine the broader utility of candidate markers, and protein identification permits understanding of their molecular basis. C3adesArg appears to lack specificity among patients with benign diseases, limiting its utility as a stand-alone tumor marker, but it may still be useful in a multimarker panel for early detection of breast cancer.

scholarly journals Proteomic profiles of unilateral cryptorchidism in pigs at different ages using MALDI-TOF mass spectrometry and in-gel digestion coupled with mass spectrometry (GeLC-MS/MS) approaches

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Nathamon Yimpring ◽  
Sittiruk Roytrakul ◽  
Janthima Jaresitthikunchai ◽  
Narumon Phaonakrop ◽  
Sucheewin Krobthong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Western Blot ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Expression Profiles ◽  
Tumor Necrosis Factor Receptor ◽  
Principal Component ◽  
Peptide Mass ◽  
Different Ages

Abstract Background Cryptorchidism is a condition that occurs when one or both testes fail to descend into the scrotum. It is a common congenital disorder, causing economic loss in pig production. However, there have been only limited studies of differential protein expression profiles in undescended testes (UDTs) in the abdomen and descended testes (DTs) in cryptorchid pigs, especially at the peptidome and proteome levels. The present study aimed to analyze the peptidome of UDTs and DTs in unilateral cryptorchid pigs aged 1–2, 6, 15 and 20 weeks and in normal testes of healthy pigs aged 1–2 and 12 weeks, using peptide mass fingerprinting and three-dimensional principal component analysis (3D-PCA) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and to identify potential protein candidates, using in-gel digestion coupled with mass spectrometry (GeLC-MS/MS). Western blot analysis was used to verify protein expression. Protein sequence was affirmed by liquid chromatography–tandem mass spectrometry. Results A PCA plot showed a discrete cluster for each sample group. Peptide mass fingerprints (PMFs) demonstrated unique peptide fragments in UDTs at different ages. A number of markedly expressed proteins from GeLC-MS/MS were identified, including the multifunctional tumor necrosis factor receptor superfamily member 18 (TNFRSF18), in DTs at 1–2 and 6 weeks and in UDTs at 15 and 20 weeks of age. Using western blot analysis, high expression of TNFRSF18 was observed in the UDTs at 15 weeks. Using the STITCH database, this protein was found to be related to apoptosis, corresponding to the previous report in the UDTs at the same age. Conclusions The present study revealed the specific PMFs and clusters for porcine cryptorchidism, and a novel protein, TNFRSF18, associated with the disease mechanism. These results could provide further insights into the pathogenesis of the disease.

scholarly journals Immunohistochemical validation of COL3A1, GPR158 and PITHD1 as prognostic biomarkers in early-stage ovarian carcinomas

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hanna Engqvist ◽  
Toshima Z. Parris ◽  
Anikó Kovács ◽  
Szilárd Nemes ◽  
Elisabeth Werner Rönnerman ◽  
...  
Keyword(s):  
Overall Survival ◽  
Protein Expression ◽  
Ovarian Carcinoma ◽  
Early Stage ◽  
Gynecological Cancer ◽  
Expression Patterns ◽  
Survival Rates ◽  
Prognostic Biomarkers ◽  
Ovarian Carcinomas ◽  
Clear Cell Ovarian Carcinoma

Abstract Background Ovarian cancer is the main cause of gynecological cancer-associated death. However, 5-year survival rates differ dramatically between the five main ovarian carcinoma histotypes. Therefore, we need to have a better understanding of the mechanisms that promote histotype-specific ovarian carcinogenesis and identify novel prognostic biomarkers. Methods Here, we evaluated the prognostic role of 29 genes for early-stage (I and II) ovarian carcinomas (n = 206) using immunohistochemistry (IHC). Results We provide evidence of aberrant protein expression patterns for Collagen type III alpha 1 chain (COL3A1), G protein-coupled receptor 158 (GPR158) and PITH domain containing 1 (PITHD1). Kaplan-Meier survival analysis revealed that COL3A1 expression was associated with shorter overall survival in the four major histotypes of epithelial ovarian carcinoma patients (P value = 0.026, HR = 2.99 (95% CI 1.089–8.19)). Furthermore, GPR158 and PITHD1 were shown to be histotype-specific prognostic biomarkers, with elevated GPR158 expression patterns in mucinous ovarian carcinoma patients with unfavorable overall survival (P value = 0.00043, HR = 6.13 (95% CI 1.98–18.98)), and an association with lower PITHD1 protein expression and unfavorable overall and disease-specific survival in clear-cell ovarian carcinoma patients (P value = 0.012, HR = 0.22 (95% CI 0.058–0.80); P value = 0.003, HR = 0.17 (95% CI 0.043–0.64)). Conclusions The novel biomarkers identified here may improve prognostication at the time of diagnosis and may assist in the development of future individualized therapeutic strategies for ovarian carcinoma patients.

Protein expression profiling in the gill of Litopenaeus vannamei (Boone, 1931) naturally infected with white spot syndrome virus

Crustaceana ◽  
2015 ◽  
Vol 88 (7-8) ◽  
pp. 747-765
Author(s):  
P. A. Valentim-Neto ◽  
A. P. M. Fraga ◽  
G. A. S. Müller ◽  
M. R. F. Marques
Keyword(s):  
Protein Expression ◽  
Litopenaeus Vannamei ◽  
White Spot Syndrome Virus ◽  
Polyacrylamide Gel Electrophoresis ◽  
Differentially Expressed ◽  
White Spot ◽  
Mortality Factor ◽  
Control Group ◽  
Peptide Mass ◽  
White Spot Syndrome

To better understand the molecular pathogenesis of white spot syndrome virus (WSSV) inLitopenaeus vannamei(Boone, 1931), the protein expression profile in gills was characterized. Farmed shrimp WSSV positive were randomly sorted based on nested PCR. The proteomic analysis of gill proteins was performed using two-dimensional electrophoresis (2-DE), with isofocalisation on an immobilized linear gradient (pH 3-10), followed by separation based on molecular weight using 12.5% denaturating polyacrylamide gel electrophoresis (SDS-PAGE). The comparative analysis of the 2-DE profile between the two groups revealed eight differentially expressed spots in gills of naturally infected shrimp. The spots were successfully identified using MALDI-TOF mass spectrometry peptide mass fingerprint. The up-regulated proteins unique to infected shrimp were identified as peptidyl-prolyl isomerase, mortality factor 4-like protein 1, calreticulin, recombination activating protein, failed axon connection protein, 40S ribosomal S2 and N-deacetylase/N-sulfotransferase. The down-regulated protein unique to non-infected shrimp (control group) was identified as an inhibitor of apoptosis. The differentially expressed proteins are involved in several important cellular processes, such as host defence and protein metabolism. The present work contributes to a better understanding of the overall molecular responses elicited by WSSV infection inL. vannamei, as well as to point out potential molecular biomarkers to evaluate the susceptibility to the virus and the sanitary status in farmed shrimp.

scholarly journals Proteomic Examination for Gluconeogenesis Pathway-Shift during Polyhydroxyalkanoate Formation in Cupriavidus necator Grown on Glycerol

2020 ◽  
Vol 7 (4) ◽  
pp. 154
Author(s):  
Nuttapol Tanadchangsaeng ◽  
Sittiruk Roytrakul
Keyword(s):  
Mass Spectrometry ◽  
Glycosyl Hydrolase ◽  
Expression Patterns ◽  
Polyacrylamide Gel Electrophoresis ◽  
Cupriavidus Necator ◽  
Production Costs ◽  
Raw Material ◽  
Short Chain ◽  
Bacterial Cells ◽  
Glucose Content

Because of availability and inexpensiveness, glycerol can be considered as a suitable raw material for polyhydroxyalkanoate (PHA) production with bacterial fermentation. Nevertheless, compared to the production of glucose as a raw precursor, PHA produced from glycerol by Cupriavidus necator was found to produce lower PHA with low bacterial growth rates. According to our study, C. necator was able to synthesize glucose-like intermediates from glycerol via gluconeogenesis. This resulted in a decrease of the cell dry weight and the yield of PHA polymers, especially in the active cell growth phase. It was indicated that glycerol used as a carbon source of the PHA synthesis pathway has glucogenesis-shift, which causes a decrease of the PHA content and productivity. In this research, we investigated the proteins that were closely expressed with the increase of the intracellular PHA and glucose content. For solving the above problem, the proteins inside the bacterial cells were analyzed and compared to the database proteins via mass spectrometry. The proteins were isolated by 1-D SDS-polyacrylamide gel electrophoresis (PAGE) technique and identified by the liquid chromatography mass spectrometry (LC-MS) technique. By using bioinformatics validation, a total number of 1361 proteins were examined and found in the culture bacterial cells. Selective protein expression was correlated with the amount of PHA at each cultivation time and generating glucose by studying the 1361 proteins was elucidated in proteomic information. The results of the cluster of proteins were found to contain 93 proteins using the multiple array viewer (MEV) program with the KMS data analysis model. Protein species with the same expression pattern for PHA and six proteins with similar expression patterns were found to be correlated with generating glucose content. The associations of the two protein groups were then determined through a Stitch program. The protein and chemical associations were analyzed both directly and indirectly through different databases. The proteins of interest were found with research data linked between glycerol and glucose. Five protein types are connecting to glucose and glycerol shift pathway, two of which are glycosyl hydrolase (H16_B1563) and short-chain dehydrogenase (H16_B0687), both of which are enzymes used to break the bonds of complex sugars, possibly related to the partial conversion of glycerol to glucose. The two proteins found in the strains used in the Cupriavidus necator H16 experiment give rise to the break down the bonds of α,α-1,1-glucoside of malto-oligosyltrehalose and short-chain sugar molecules such as mannitol (C6H14O6), respectively. In this research, finding the associated expression proteins which is involved in changing the pathway of gluconeogenesis shift to PHA synthesis will be useful information on genetically modifying microorganisms to produce PHA more efficiently, leading to reduction of the production costs.

Study on the Mechanisms of CML Blast Crisis by Comparative Proteome Analysis.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4770-4770
Author(s):  
Xiaoli Liu ◽  
Qingfeng Du ◽  
Song Zhang ◽  
Rong Li ◽  
Feng Yao ◽  
...  
Keyword(s):  
Protein Expression ◽  
Blast Crisis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Chronic Phase ◽  
Proteome Analysis ◽  
Terminal Phase ◽  
Proteasome Subunit ◽  
Peptide Mass ◽  
Significant Difference ◽  
Leukotriene A4

Abstract The clinical course of chronic myeloid leukemia(CML)is characteristically triphasic, comprising chronic and accelerated phases and blast crisis. Chronic phase(CP) is characterized by the Ph chromosome as the sole genetic abnormality and blast crisis(BC), which is the terminal phase of CML, often associated with additional chromosomal and molecular secondary changes. Although CML is probably the most extensively studied human malignancy, the mechanisms of CML blast crisis are still poorly understood. In current study, we analyzed the changes of protein expression between CML-CP(25 cases) and CML-BC(20 cases) by Two-dimensional polyacrylamide gel electrophoresis(2-D PAGE). Compared with that of CML-CP, 33 proteins’ intensities of CML-BC were found to have significant difference including 23 increasing and 13 decreasing. 15 proteins were identified by peptide mass fingerprint in combination with database searching including proteasome activator complex, hnRNP, annexin A4, serine proteinase inhibitor, annexin A1, GAPDH, RhoGDI, enolase, proteasome subunit 6a, GTP binding protein, leukotriene A4 hydrolase, Rac-RhoGDI, thioredoxin, proteasome subunit 4β and DJ-1 protein, and the functions of these proteins involve cell signal transduction, apoptosis, proliferation and transcription. In conclusion, our study provided a profile of protein expression difference between CML-CP and CML-BC and contributed to understand the mechanisms of CML blast crisis.

Analysis of protein expression patterns in Barrett’s esophagus using Maldi mass spectrometry, in search of malignancy biomarkers

2005 ◽  
Vol 18 (3) ◽  
pp. 170-176 ◽  
Author(s):  
J. M. Streitz ◽  
M. T. Madden ◽  
S. S. Marimanikkuppam ◽  
T. P. Krick ◽  
W. L. Salo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Barrett’S Esophagus ◽  
Barrett's Esophagus ◽  
Expression Patterns ◽  
Maldi Mass Spectrometry

Diurnal protein expression in blood revealed by high throughput mass spectrometry proteomics and implications for translational medicine and body time of day

2007 ◽  
Vol 293 (3) ◽  
pp. R1430-R1437 ◽  
Author(s):  
Tami A. Martino ◽  
Nazneen Tata ◽  
Georg A. Bjarnason ◽  
Marty Straume ◽  
Michael J. Sole
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
High Throughput ◽  
De Novo ◽  
Expression Patterns ◽  
Time Of Day ◽  
The Body ◽  
Molecular Testing ◽  
Ionization Mass ◽  
Blood Proteins

Molecular gene cycling is useful for determining body time of day (BTOD) with important applications in personalized medicine, including cardiovascular disease and cancer, our leading causes of death. However, it impractically requires repetitive invasive tissue sampling that is obviously not applicable for humans. Here we characterize diurnal protein cycling in blood using high-throughput proteomics; blood proteins are easily accessible, minimally invasive, and can importantly serve as surrogates for what is happening elsewhere in the body in health and disease. As proof of the concept, we used normal C57BL/6 mice maintained under regular 24-h light and dark cycles. First, we demonstrated fingerprint patterns in 24-h plasma, revealed using surface-enhanced laser desorption and ionization (SELDI). Second, we characterized diurnal cycling proteins in blood using chromatography and tandem electrospray ionization mass spectrometry. Importantly, we noted little association between the cycling blood proteome and tissue transcriptome, delineating the necessity to identify de novo cycling proteins in blood for measuring BTOD. Furthermore, we explored known interaction networks to identify putative functional pathways regulating protein expression patterns in blood, thus shedding new light on our understanding of integrative physiology. These studies have profound clinical significance in translating the concept of BTOD to the practical realm for molecular diagnostics and open new opportunities for clinically relevant discoveries when applied to ELISA-based molecular testing and/or point-of-care devices.

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