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Sedic M, Gethings LA, Vissers JPC, Shockcor JP, McDonald S, Vasieva O, Lemac M, Langridge JI, Batinić D, Pavelić SK. Label-free mass spectrometric profiling of urinary proteins and metabolites from paediatric idiopathic nephrotic syndrome. Biochem Biophys Res Commun 2014; 452:21-6. [PMID: 25150443 DOI: 10.1016/j.bbrc.2014.08.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 08/04/2014] [Indexed: 01/20/2023]
Abstract
Idiopathic nephrotic syndrome (INS) is caused by renal diseases that increase the permeability of the glomerular filtration barrier without evidence of a specific systemic cause. The aim of the present work was to reveal inherent molecular features of INS in children using combined urinary proteomics and metabolomics profiling. In this study, label-free mass spectrometric analysis of urinary proteins and small molecule metabolites was carried out in 12 patients with INS versus 12 sex- and age-matched control subjects with normal renal function. Integration and biological interpretation of obtained results were carried out by Ingenuity IPA software. Validation of obtained proteomics data was carried out by Western blot method. Proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000765. This study indicates for the first time that paediatric INS is associated with up-regulation of afamin, hydroxyphenylacetate and uridine, and concomitant down-regulation in glutamine and phenylalanine levels, and many of these molecular species were previously shown to be involved in oxidative stress. Further studies in larger patient population are underway to investigate the role of oxidative stress in renal injury in paediatric INS.
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Affiliation(s)
- Mirela Sedic
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Lee A Gethings
- Waters Corporation, MS Technologies, Manchester, United Kingdom
| | | | | | | | - Olga Vasieva
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Maja Lemac
- Division of Nephrology, Department of Pediatrics, Zagreb University Hospital Centre, Zagreb, Croatia
| | | | - Danica Batinić
- Division of Nephrology, Department of Pediatrics, Zagreb University Hospital Centre, Zagreb, Croatia
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Sedic M, Kraljevic Pavelic S, Cindric M, Vissers JPC, Peronja M, Josic D, Cuk M, Fumic K, Pavelic K, Baric I. Plasma biomarker identification in S-adenosylhomocysteine hydrolase deficiency. Electrophoresis 2011; 32:1970-5. [PMID: 21732553 DOI: 10.1002/elps.201000556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 11/09/2022]
Abstract
S-Adenosylhomocysteine hydrolase (AHCY) deficiency is a rare congenital disorder in methionine metabolism clinically characterized by white matter atrophy, delayed myelination, slowly progressive myopathy, retarded psychomotor development and mildly active chronic hepatitis. In the present study, we utilized a comparative proteomics strategy based on 2-DE/MALDI-MS and LC/ESI-MS to analyze plasma proteins from three AHCY-deficient patients prior to and after receiving dietary treatment designed to alleviate disease symptoms. Obtained results revealed candidate biomarkers for the detection of myopathy specifically associated with AHCY deficiency, such as carbonic anhydrase 3, creatine kinase, and thrombospondin 4. Several proteins mediating T-cell activation and function were identified as well, including attractin and diacylglycerol kinase α. Further validation and functional analysis of identified proteins with clinical value would ensure that these biomarkers make their way into routine diagnosis and management of AHCY deficiency.
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Affiliation(s)
- Mirela Sedic
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
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Kraljevic Pavelic S, Sedic M, Bosnjak H, Spaventi S, Pavelic K. Metastasis: new perspectives on an old problem. Mol Cancer 2011; 10:22. [PMID: 21342498 PMCID: PMC3052211 DOI: 10.1186/1476-4598-10-22] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/22/2011] [Indexed: 12/23/2022] Open
Abstract
Many hypotheses have been postulated to explain the intricate nature of the metastatic process, but none of them completely accounted for the actual biological and clinical observations. Consequently, metastasis still remains an open issue with only few metastasis-inducing proteins experimentally validated so far. Recently proposed novel metastatic model, where serial and parallel metastatic processes are adequately integrated, might help to bridge the current gap between experimental results and clinical observations. In addition, the identification, isolation and molecular characterization of cancer stem cells, a population of the cells within the tumour mass able to proliferate, self-renew and induce tumorigenesis, will shed new light on the complex molecular events mediating metastasis, invasion and resistance to therapy. Understanding the molecular basis of these tumour characteristics will usher in a new age of individualized cancer therapy. In this review article, we will provide a current overview of molecular mechanisms underpinning metastasis, and discuss recent findings in this field obtained by global molecular profiling strategies such as proteomics.
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Kraljevic Pavelic S, Sedic M, Hock K, Vucinic S, Jurisic D, Gehrig P, Scott M, Schlapbach R, Cacev T, Kapitanovic S, Pavelic K. An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease. J Pathol 2009; 217:524-33. [DOI: 10.1002/path.2483] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sedic M, Poznic M, Gehrig P, Scott M, Schlapbach R, Hranjec M, Karminski-Zamola G, Pavelic K, Kraljevic Pavelic S. Differential antiproliferative mechanisms of novel derivative of benzimidazo[1,2-alpha]quinoline in colon cancer cells depending on their p53 status. Mol Cancer Ther 2008; 7:2121-32. [PMID: 18645022 DOI: 10.1158/1535-7163.mct-07-2261] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the present article, we describe a mechanistic study of a novel derivative of N-amidino-substituted benzimidazo[1,2-alpha]quinoline in two human colorectal cancer cell lines differing in p53 gene status. We used a proteomic approach based on two-dimensional gel electrophoresis coupled with mass spectrometry to complement the results obtained by common molecular biology methods for analyzing cell proliferation, cell cycle, and apoptosis. Tested quinoline derivative inhibited colon cancer cell growth, whereby p53 gene status seemed to be critical for its differential response patterns. DNA damage and oxidative stress are likely to be the common triggers of molecular events underlying its antiproliferative effects. In HCT 116 (wild-type p53), this compound induced a p53-dependent response resulting in accumulation of the G(1)- and S-phase cells and induction of apoptosis via both caspase-3-dependent and caspase-independent pathways. Quinoline derivative triggered transient, p53-independent G(2)-M arrest in mutant p53 cells (SW620) and succeeding mitotic transition, whereby these cells underwent cell death probably due to aberrant mitosis (mitotic catastrophe). Proteomic approach used in this study proved to be a valuable tool for investigating cancer cell response to newly synthesized compound, as it specifically unraveled some molecular changes that would not have been otherwise detected (e.g., up-regulation of the p53-dependent chemotherapeutic response marker maspin in HCT 116 and impairment in ribosome biogenesis in SW620). Finally, antiproliferative effects of tested quinoline derivative on SW620 cells strongly support its possible role as an antimetastatic agent and encourage further in vivo studies on the chemotherapeutic potential of this compound against colorectal carcinoma.
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Affiliation(s)
- Mirela Sedic
- Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia.
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Kraljevic S, Sedic M, Scott M, Gehrig P, Schlapbach R, Pavelic K. Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view? Cancer Treat Rev 2006; 32:619-29. [PMID: 17069979 DOI: 10.1016/j.ctrv.2006.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Revised: 09/05/2006] [Accepted: 09/07/2006] [Indexed: 02/05/2023]
Abstract
Regardless of continuous advances in technology and expansion of the knowledge in the field of genomic information, cancer still remains one of the leading causes of death in developed countries for many reasons, including non-selectiveness of commonly used anti-cancer drugs that often influence non-specific rather than tumour-specific targets. As cancer cells are characterized by the ability to divide and multiply in an uncontrolled manner whereby a set of specific proteins modulate cell division processes, proteomics seems to be a suitable tool for seeking out molecular mediators of anti-cancer drugs action and resistance, thus improving chemotherapy outcome. This review will focus on the recent knowledge of the molecular mechanisms involved in the anti-cancer drugs response revealed by the proteomics tools. In addition, we will touch upon the effects of "gene drugs" with p53 and p21(waf1/cip1) genes on the protein complement of tumour cells assessed by the two-dimensional gel electrophoresis combined with mass spectrometry. Such studies could substantially contribute to further drug optimization prior to its clinical use and represent an important but still small step in the long way of drug discovery. However, fluctuations in protein expression, distribution, posttranslational modifications, interactions, functions and compartmentalization make it difficult to use exclusively expression proteomics data without putting it in broader biological context. Thus, the challenge today is to shift from the identification of drug response and disease biomarkers to more time-consuming process of revealing the biochemical mechanism that connects a specific protein with a disease or cellular response to a drug.
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Affiliation(s)
- Sandra Kraljevic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Bijenicka Cesta 54, 10002 Zagreb, Croatia.
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Pavelic K, Kralj M, Kraljevic S, Sedic M. Global Approach to Biomedicine: Functional Genomics and Proteomics. EJIFCC 2005; 16:22-26. [PMID: 29942230 PMCID: PMC6008969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kresimir Pavelic
- Corresponding author’s address: Kresimir Pavelic, MD, PhD Head of the Division of Molecular Medicine Rudjer Boskovic Institute Bijenicka cesta 54 POB 180 HR-10002 Zagreb CROATIA
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Ribar S, Mesaric M, Sedic M. Sphingoid bases as possible diagnostic parameters. Croat Med J 2003; 44:165-70. [PMID: 12698507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
AIM To determine the concentrations and ratios of sphingoid bases, sphinganine and sphingosine, in the serum and urine of healthy individuals, as a basis for the normal value range, which may be useful in the diagnosis of diseases characterized by sphingolipid metabolism impairment. Possible sex differences were also investigated, as well as effects of hormonal changes on sphingoid base concentrations during pregnancy or menopause. METHOD Sphingolipids were extracted from the serum and urine and hydrolyzed. Sphinganine and sphingosine were determined by high performance liquid chromatography. The analysis included serum and urine samples of 20 men and 20 women, and urine samples of 5 healthy postmenopausal and 5 healthy pregnant women. RESULTS Serum concentrations of free and total sphingoid bases showed no major variations in healthy individuals of both sexes: total sphingosine 28.28-/+8.96 x 10(3) pmol/mL in men and 22.52-/+10.19 x 10(3) pmol/mL in women (p=0.080); total sphinganine 0.61-/+0.15 x 10(3) pmol/mL in men and 0.58-/+0.25 x 10(3) pmol/mL in women (p=0.574). Urine concentrations showed greater variability. Hormonal changes associated with menopause or pregnancy significantly decreased the urinary concentrations of total sphinganine in postmenopausal women, and increased free sphinganine/sphingozine ratio. CONCLUSION Serum but not urine concentrations of sphingoid bases could be used as a sensitive indicator in the diagnosis of the diseases associated with sphingolipid metabolism impairment.
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Affiliation(s)
- Slavica Ribar
- Department of Chemistry and Biochemistry, Zagreb University School of Medicine, Zagreb, Croatia
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