Cancer Immunomics: From Serological Proteome Analysis to Multiple Affinity Protein Profiling

2007 ◽  
Vol 1107 (1) ◽  
pp. 223-230 ◽  
Author(s):  
J. HARDOUIN ◽  
J.-P. LASSERRE ◽  
L. SYLVIUS ◽  
R. JOUBERT-CARON ◽  
M. CARON
Keyword(s):  
Proteome Analysis ◽  
Protein Profiling

Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling

2018 ◽  
Vol 90 (23) ◽  
pp. 14003-14010 ◽  
Author(s):  
Xi Shao ◽  
Xuantang Wang ◽  
Sheng Guan ◽  
Haizhu Lin ◽  
Guoquan Yan ◽  
...  
Keyword(s):  
Single Cell ◽  
Proteome Analysis ◽  
Single Cell Protein ◽  
Protein Profiling ◽  
Cell Protein

scholarly journals Cell Shape and Cardiosphere Differentiation: A Revelation by Proteomic Profiling

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Nanako Kawaguchi ◽  
Mitsuyo Machida ◽  
Kota Hatta ◽  
Toshio Nakanishi ◽  
Yohtaroh Takagaki
Keyword(s):  
Stem Cells ◽  
Stress Proteins ◽  
Embryonic Stem ◽  
Proteome Analysis ◽  
Protein Profiling ◽  
Proteomic Profiling ◽  
Low Oxygen ◽  
Cellular Functions ◽  
Proliferation And Differentiation ◽  
Undifferentiated Cells

Stem cells (embryonic stem cells, somatic stem cells such as neural stem cells, and cardiac stem cells) and cancer cells are known to aggregate and form spheroid structures. This behavior is common in undifferentiated cells and may be necessary for adapting to certain conditions such as low-oxygen levels or to maintain undifferentiated status in microenvironments including stem cell niches. In order to decipher the meaning of this spheroid structure, we established a cardiosphere clone (CSC-21E) derived from the rat heart which can switch its morphology between spheroid and nonspheroid. Two forms, floating cardiospheres and dish-attached flat cells, could be switched reversibly by changing the cell culture condition. We performed differential proteome analysis studies and obtained protein profiles distinct between spherical forms and flat cells. From protein profiling analysis, we found upregulation of glycolytic enzymes in spheroids with some stress proteins switched in expression levels between these two forms. Evidence has been accumulating that certain chaperone/stress proteins are upregulated in concert with cellular changes including proliferation and differentiation. We would like to discuss the possible mechanism of how these aggregates affect cell differentiation and/or other cellular functions.

scholarly journals In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Maria Pernemalm ◽  
AnnSofi Sandberg ◽  
Yafeng Zhu ◽  
Jorrit Boekel ◽  
Davide Tamburro ◽  
...  
Keyword(s):  
Human Plasma ◽  
Genomic Sequence ◽  
Proteome Analysis ◽  
Protein Profiling ◽  
Single Amino Acid ◽  
Sequence Information ◽  
Plasma Proteome ◽  
Multiple Protein ◽  
Protein Variants ◽  
Human Plasma Proteome

Here, we present a method for in-depth human plasma proteome analysis based on high-resolution isoelectric focusing HiRIEF LC-MS/MS, demonstrating high proteome coverage, reproducibility and the potential for liquid biopsy protein profiling. By integrating genomic sequence information to the MS-based plasma proteome analysis, we enable detection of single amino acid variants and for the first time demonstrate transfer of multiple protein variants between mother and fetus across the placenta. We further show that our method has the ability to detect both low abundance tissue-annotated proteins and phosphorylated proteins in plasma, as well as quantitate differences in plasma proteomes between the mother and the newborn as well as changes related to pregnancy.

Comparative serum proteome analysis reveals potential early pregnancy-specific protein biomarkers in pigs

2019 ◽  
Vol 31 (3) ◽  
pp. 613 ◽  
Author(s):  
Ankan De ◽  
Mohammad Ayub Ali ◽  
Tukheswar Chutia ◽  
Suneel Kumar Onteru ◽  
Parthasarathi Behera ◽  
...  
Keyword(s):  
Early Pregnancy ◽  
Inflammatory Responses ◽  
Proteome Analysis ◽  
Specific Protein ◽  
Protein Profiling ◽  
Differentially Expressed ◽  
Label Free ◽  
Protein Biomarkers ◽  
Serum Proteome ◽  
Pregnancy Zone Protein

In this study, the comparative serum proteome profile of Day 5, 12 and 16 of gestation, representing three early embryonic events, namely formation, elongation and implantation of blastocysts, and non-pregnant control were explored by a label-free quantitation-based mass spectrometric approach to identify early pregnancy biomarkers in pigs. A total of 131 proteins were identified with respect to different groups, out of which 105 were found to be differentially expressed proteins (DEPs). Among the DEPs, 54 and 66 proteins were found to be up and downregulated respectively in early pregnancy groups (fold change >2) and the maximum number of upregulated proteins was observed in the Day 12 pregnancy stage. Functional classification and pathway analysis of the DEPs revealed involvement of most of the proteins in complement and coagulation cascades, metabolic processes and immune and inflammatory responses. Proteins such as glutathione peroxidise (GPX), pregnancy zone protein (PZP), thrombospondin-1 (THBS1), α-1-antitrypsin (AAT) and mannose-binding lectin C (MBLC) were differentially expressed during early pregnancy and actively involved in different pregnancy-related activities. To the best of our knowledge, this is the first report on comparative serum protein profiling of different early pregnancy stages in pigs and our results provide a set of proteins that can be used as potential biomarkers for early pregnancy diagnosis in pigs.

scholarly journals Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E

2022 ◽  
Vol 12 ◽  
Author(s):  
Thomas Klaus ◽  
Sabrina Ninck ◽  
Andreas Albersmeier ◽  
Tobias Busche ◽  
Daniel Wibberg ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Recombinant Protein Expression ◽  
Proteome Analysis ◽  
Optimal Growth ◽  
Enzyme Characterization ◽  
Protein Profiling ◽  
Glycoside Hydrolases ◽  
General Applicability ◽  
Xylanolytic Activity ◽  
Complementary Approach

Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6–7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles.

scholarly journals Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Deep Chandra Suyal ◽  
Divya Joshi ◽  
Saurabh Kumar ◽  
Ravindra Soni ◽  
Reeta Goel
Keyword(s):  
Low Temperature ◽  
Nitrogen Deficiency ◽  
Proteome Analysis ◽  
Pentose Phosphate ◽  
Protein Profiling ◽  
Adaptive Responses ◽  
Response Regulators ◽  
Differential Proteomics ◽  
First Time ◽  
Atp Binding Protein

AbstractProtein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.

scholarly journals Skeletal Malformation on Balb-C Foetal Mice (Mus musculus) Administered by Immature Pineapple Fruits Extract

2017 ◽  
Vol 3 (4) ◽  
pp. 86
Author(s):  
Fila Prasetyawati ◽  
Abdul Gofur ◽  
Umie Lestari
Keyword(s):  
Proteome Analysis ◽  
Molecular Techniques ◽  
Protein Profiling ◽  
Blue Staining ◽  
Alcian Blue Staining ◽  
Protein Profiles ◽  
Foetal Development ◽  
Alizarin Red ◽  
Medicinal Uses ◽  
Skeletal Malformation

<p class="Els-Abstract-text">Nutrients for pregnant woman affect the development of foetus in the womb. Pineapple has bromelain enzyme which benefit in medicinal uses, but it can be considered as teratogenic agents due to its proteolytic activities. The period of organogenesis is the critical period in foetal development. Examination of foetal anatomy is still a fundamental part of teratological studies despites of modern molecular techniques. Molecular techniques can be done by conducting the skeletal proteome analysis to evaluate the teratogenic effects on the foetal skeleton. This research was performed to examine the effect of immature pineapple fruits extract on the occurrence of skeletal malformation and identify the protein profiles of skeleton on Balb-C foetal mice. Pregnant mice were administered by immature pineapple fruits extract orally by gavage with doses 0 %, 20 %, 40 %, 60 % and 80 % at day 6 d to 15 d of gestation. Skeletal malformation observed after Alizarin red-Alcian blue staining, and SDS-PAGE was conducted to identify the protein profiles of foetal skeleton. Immature pineapple fruits extract caused the decreasing of weight and length of litter, causing hemorrhage, ossification retardation on sternebra, metacarpal, metatarsal, caudal vertebrae, undulated costae and asymmetric sternebra. Protein profiling analysis showed that skeletal proteins at molecular weight of 32 kDa, 35 kDa, 42 kDa and 49 kDa did not found in foetal mice administered by immature pineapple fruits extract.</p><div><p class="Els-keywords"><em> </em></p><p class="Els-keywords"><strong>Keywords:</strong> bromelain; immature pineapple fruits; skeletal malformation; skeletal proteome analysis.</p></div>

Proteome analysis of cerebrospinal fluid in patients with Multiple System Atrophy (MSA)

2008 ◽  
Vol 35 (S 01) ◽  
Author(s):  
S Werz ◽  
V Lehmensiek ◽  
S Süssmuth ◽  
H Mogel ◽  
J Brettschneider ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Multiple System Atrophy ◽  
Proteome Analysis

Protective effects of soy-isoflavones in cardiovascular disease

2008 ◽  
Vol 28 (01/02) ◽  
pp. 85-88 ◽  
Author(s):  
D. Fuchs ◽  
H. Daniel ◽  
U. Wenzel
Keyword(s):  
Cardiovascular Disease ◽  
Endothelial Cells ◽  
Molecular Mechanisms ◽  
Dietary Intervention ◽  
Mononuclear Cells ◽  
Oxidized Ldl ◽  
Proteome Analysis ◽  
Soy Isoflavones ◽  
Protective Effects ◽  
Estrogen Production

SummaryEpidemiological studies indicate that the consumption of soy-containing food may prevent or slow-down the development of cardiovascular disease. In endothelial cells application of a soy extract or a combination of the most abundant soy isoflavones genistein and daidzein both inhibited apoptosis, a driving force in atherosclerosis development, when applied in combination with oxidized LDL or homocysteine. Proteome analysis revealed that the stressorinduced alteration of protein expression profile was reversed by the soy extract or the genistein/daidzein mixture. Only few protein entities that could be functionally linked to mitochondrial dysfunction were regulated in common by both application forms of isoflavones. A dietary intervention with isoflavone-enriched soy extract in postmenopausal women, who generally show strongly increased cardiovascular risk due to diminished estrogen production, led to significant alterations in the steady state levels of proteins from mononuclear blood cells. The proteins identified by proteome analysis revealed that soy isoflavones may increase the anti-inflammatory response in blood mononuclear cells thereby contributing to the atherosclerosispreventive activities of a soy-rich diet. Conclusion: By proteome analysis protein targets were identified in vitro in endothelial cells that respond to soy isoflavones and that may decipher molecular mechanisms through which soy products exert their protective effects in the vasculature.

Differentiation of Tumour from Normal Colorectal Tissue by SELDI-MS Protein Profiling

Endoscopy ◽  
2004 ◽  
Vol 36 (05) ◽  
Author(s):  
AM Lennon ◽  
D Stuart ◽  
AC Tan ◽  
E Fox ◽  
KS Sheahan ◽  
...  
Keyword(s):  
Protein Profiling ◽  
Colorectal Tissue ◽  
Normal Colorectal Tissue
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