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Plasma Proteome Profiling of CML in Pakistan

ABSTRACT: Systematic characterization of the plasma proteome in healthy and diseased state may uncover the potential biomarkers of disease diagnosis, prognosis and/or relapse detection. We, in this research project, have employed two-dimensional gel electrophoresis in conjunction with mass spectrometry-based analysis in a proteome-wide search for the identification of biomarkers of chronic-phase chronic myeloid leukemia (CP-CML).

INSTRUMENT(S): ultraflex

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood Plasma

DISEASE(S): Chronic Myeloid Leukemia

SUBMITTER: Muhammad Akhtar

LAB HEAD: Prof. Dr. M. Waheed Akhtar

PROVIDER: PXD002757 | Pride | 2017-01-30

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	AACT.fasta	Fasta
	CD5L.fasta	Fasta
	CPCML.png	Other
	FTTAoeEOE.dat	Other
	FTTAoeEeS.dat	Other

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Publications

CD5 molecule-like and transthyretin as putative biomarkers of chronic myeloid leukemia - an insight from the proteomic analysis of human plasma.

Fatima Iram I Sadaf Saima S Musharraf Syed Ghulam SG Hashmi Naghma N Akhtar Muhammad Waheed MW

Scientific reports 20170124

Better and sensitive biomarkers are needed to help understand the mechanism of disease onset, progression, prognosis and monitoring of the therapeutic response. Aim of this study was to identify the candidate circulating markers of chronic-phase chronic myeloid leukemia (CP-CML) manifestations, having potential to develop into predictive- or monitoring-biomarkers. A proteomic approach, two-dimensional gel electrophoresis in conjunction with mass spectrometry (2DE-MS), was employed for this purpo ...[more]

PMID: 28117336

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Project description:Ovarian cancer is one of the leading causes of death from cancer in females, worldwide. An early diagnosis of ovarian carcinoma is likely to improve clinical outcome of patients in terms of reduced morbidity and mortality. The objective of our project is the proteomic analysis of ovarian malignant and non-malignant tissue samples to find potential biomarkers of disease diagnosis and prognosis that can be assessed non-invasively through patient plasma/serum screening. In this project, we have used a methodical approach involving 2-dimensional gel electrophoresis in conjunction with MALDI-TOF MS analysis followed by immunological validation of the selected markers by western blotting and ELISA for identification of biomarkers of ovarian cancer. The associated research paper is in preparation.

2021-09-08 | PXD014352 | Pride

Tissue Proteome Profiling of Ovarian cancer in Pakistani Population.

Project description:Ovarian cancer is the 5th main cause of death from cancer in females, worldwide. An early and accurate diagnosis of ovarian carcinoma is likely to improve clinical outcome of patients in terms of reduced morbidity and mortality. The objective of our project is the proteome profiling of ovarian malignant and non-malignant tissue samples to find potential biomarkers of disease diagnosis and prognosis. In this project, we have used a systematic protein profiling approach involving 2-dimensional gel electrophoresis coupled with MALDI-TOF MS analysis for identification of biomarkers of ovarian cancer. The associated research paper is in preparation.

2019-11-27 | PXD013827 | Pride

Sex Impacts Cardiac Function and the Proteome Response to Thyroid Hormone in Aged Mice

Project description:Background: Sex and age have substantial influence on thyroid function. Sex influences the risk and clinical expression of thyroid disorders (TDs), with age a proposed trigger for the development of TDs. Cardiac function is affected by thyroid hormone levels with gender differences. Accordingly, we investigated the proteomic changes involved in sex based cardiac responses to thyroid dysfunction in elderly mice. Methods: Aged (18-20 months) male and female C57BL/6 mice were fed diets to create euthyroid, hypothyroid, or hyperthyroid states. Serial echocardiographs were performed to assess heart function. Proteomic changes in cardiac protein profiles were assessed by 2-D DIGE and LC-MS/MS, and a subset confirmed by immunoblotting. Results: Serial echocardiographs showed ventricular function remained unchanged regardless of treatment. Heart rate and size increased (hyperthyroid) or decreased (hypothyroid) independent of sex. Pairwise comparison between the six groups identified 55 proteins (≥ 1.5-fold difference and p < 0.1). Compared to same-sex controls 26/55 protein changes were in the female hypothyroid heart, whereas 15/55 protein changes were identified in the male hypothyroid, and male and female hyperthyroid heart. The proteins mapped to oxidative phosphorylation, tissue remodeling and inflammatory response pathways. Conclusion: We identified both predicted and novel proteins with gender specific differential expression in response to thyroid hormone status, providing a catalogue of proteins associated with thyroid dysfunction. Pursuit of these proteins and their involvement in cardiac function will expand our understanding of mechanisms involved in sex-based cardiac response to thyroid dysfunction.

2020-12-23 | PXD022557 | Pride

Proteomic analysis of plasma membrane and tonoplast from the leaves of a mangrove plant Avicennia officinalis

Project description:We used gel electrophoresis coupled with LC-MS based proteomics to identify key transport proteins in the plasma membrane (PM) and tonoplast fractions of Avicennia officinalis leaves. This was part of our attempts to understand salt tolerance and secretion in mangrove plant species. PM and tonoplast proteins were purified using two-aqueous phase partitioning and density gradient centrifugation, respectively. Thirty of the 154 PM proteins and 31 of the 118 tonoplast proteins identified were predicted to have transmembrane domains. About 90% of the identified proteins could be classified based on their functions. The major classes of proteins were predicted to be involved in transport, metabolic processes, signal transduction and defense /stress response, while a few of the proteins were predicted to be involved in membrane trafficking. The main classes of transporter proteins identified included H+-ATPases, ATP-binding cassette transporters (ABC) and aquaporins, all of which could play a role in salt secretion. These data will serve as the baseline membrane proteomic dataset for Avicennia species. Further, this information can contribute to future studies on understanding the mechanism of salt tolerance in halophytes in addition to salt secretion in mangroves.

2014-11-18 | PXD000837 | Pride

Protective cellular mechanism of estrogen against kidney stone formation: A proteomics approach and functional validation

Project description:Kidney stone disease is influenced by multiple factors, including but not limited to age, gender, genetic background, hydration status, diet and drug. Regarding the gender, epidemiologic data across the world has shown that females at the reproductive age (15-49 years) have lower incidence/prevalence of kidney stone disease approximately 1.5-2.5 folds as compared to males at the same age. However, this gap is narrower in the postmenopausal age, whereas the postmenopausal females with higher serum estrogen levels are less likely to have kidney stones. Furthermore, female stone formers (patients with kidney stones) are associated with lower estrogen levels. Therefore, estrogen has been proposed to serve as the protective hormone against kidney stone disease. However, the precise mechanisms underlying such protective effects of estrogen remain unclear and require further investigations. This study thus investigated the effects of estradiol (which is the most prevalent and potent form of estrogen in females at the reproductive age) on cellular proteome of renal tubular cells using a proteomics approach.

2019-09-09 | PXD014768 | Pride

Ocean acidification and warming impact proteome of early Crassostrea gigas larvae

Project description:Increasing atmospheric CO2 raises sea surface temperatures and results in ocean acidification, which will impact upon calcifying marine organisms, such as the commercially and ecologically important Pacific oyster (Crassostrea gigas). Larval stages of development are particularly sensitive to such stressors and may represent population bottlenecks. A two-dimensional electrophoresis (2-DE) proteomic approach was used to investigate the response of 40 hour C. gigas larvae to ocean acidification and warming, and to relate protein expression to phenotypic variation in size and calcification. Larvae were reared at two pHs (8.1 and 7.9) and two temperatures (20°C and 22°C), and comparisons carried out between the four possible treatment combinations. In total 22 differentially expressed spots, corresponding to 18 proteins, were identified by nano-liquid chromatography tandem mass spectrometry. These proteins had roles in metabolism, biomineralisation, intra- and extra-cellular matrix formation and as molecular chaperones. Thirteen of these spots responded to acidification, of which 11 showed reduced expression during acidification. Declines in ATP synthase, arginine kinase and other metabolic proteins suggest metabolic depression occurred during acidification and reduced protein synthesis. In contrast, 6 of 7 proteins that were differentially expressed during warming showed increased expression. Among these were molecular chaperones including protein disulphide isomerase (PDI) and Grp78. Concurrent acidification and warming appeared to mitigate some proteomic changes and negative phenotypic effects observed in acidification at 20°C; however, differential expression of nine proteins and other temperature-independent effects on calcification phenotypes suggest that larval responses to multiple stressors will be complex.

2022-03-01 | PXD002316 | Pride

Identification of differentially expressed proteins during the fermentation of Saccharopolyspora erythraea

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The proteome of germlings from urediniospores of Puccinia triticina

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Project description:The Pacific oyster Crassostrea gigas is a sessile animal that undergoes highly dynamic and stressful environmental constraints all along its life in the intertidal zone and estuaries. We analyzed the physiological effects induced by low environmental concentrations of two pesticides, metconazole (0.2 and 2 µg L-1) or isoproturon (0.1 and 1 µg L-1), or in mix (0.2 and 0.1 µg L-1 respectively) known to be encountered by oysters in the field. At such trace-level, metconazole and isoproturon induced a metabolic stress, reflected by an important over-activation of the sensing-kinase AMP-activated kinase (AMPK). Such deregulation reflect alteration of energy management, since the sensing-molecule AMPK plays a key role in C. gigas energetic metabolism, as well as alteration in the adaptation to environmental stress, given its role in hypoxia. Neither pesticide had any effect on eco-physiological parameters during the 14 days-experiment: filtration rate, food consumption, growth, and available energy reserves remained unchanged. In contrast, using two-dimensional electrophoresis, we identified changes in proteins that belong to energetic metabolism and cytoskeletal induced by metconazole or isoproturon. Analyses of antioxidant enzymes revealed an increase in oxidative stress pathway in superoxide dismutase and catalase in some conditions. Taken together, our results proved that trace-level environmental concentrations of metconazole or isoproturon provoke important deleterious effects at the biochemical level in oyster, by inducing a metabolic stress and oxidative stress response. Such alterations were not directly reflected at the level of the whole organism when measuring eco-physiological parameters. Identifying the impacts of pesticides at environmental concentrations using biochemical approaches is thus a promising field of research to improve monitoring processes.

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