1
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Qianman B, Wupuer A, Jiasharete T, Luo B, Nihemaiti M, Jielile J. iTRAQ-based proteomics reveals potential markers and treatment pathways for acute Achilles tendon rupture. J Orthop Surg Res 2023; 18:852. [PMID: 37946221 PMCID: PMC10636927 DOI: 10.1186/s13018-023-04346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Due to its limited blood supply and irregular mechanical loading, the Achilles tendon is the most frequently ruptured tendon. Despite the rising incidence of acute Achilles tendon rupture (AATR), the optimal treatment remains controversial. Missed diagnoses and delayed treatments lead to poor outcomes and limited treatment options. This study aimed to identify potential biomarkers for diagnosing and developing therapies for AATR. METHODS We employed the coupled isobaric tag for relative and absolute quantitation-liquid chromatography-electrospray ionization-tandem mass spectrometry approach to investigate protein expression in tissues from AATR patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify differentially expressed proteins (DEPs) between AATR patients and healthy individuals. A protein-protein interaction (PPI) network of DEPs was constructed using the Search Tool for the Retrieval of Interacting Genes. The screened hub genes were selectively verified by immunohistochemical staining. RESULTS We identified 410 DEPs between AATR patients and controls. The DEPs were significantly enriched in GO terms such as the extracellular region, extracellular region part, and defense response, as well as KEGG pathways, including complement and coagulation cascades, focal adhesion, and regulation of actin cytoskeleton. The main hub nodes in the PPI network comprised fibronectin 1 (FN1), major histocompatibility complex, class I, B (HLA-B), filamin A (FLNA), heat shock 27-kDa protein 1 (HSPB1), heat shock protein family A member 5 (HSPA5), apolipoprotein A4 (APOA4), and myosin IC (MYO1C). Although APOA4 and collagens I, II, and III were detectable in healthy tendons, immunohistochemical staining confirmed higher expression of these proteins in the acutely ruptured Achilles tendon. CONCLUSIONS Our findings lay a foundation for further molecular studies of AATR. Inflammation and age-related degeneration may contribute to the pathogenesis of AATR. Moreover, the identified DEPs could be potential biomarkers for AATR diagnosis and treatment.
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Affiliation(s)
- Bayixiati Qianman
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Aikeremu Wupuer
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Tuomilisi Jiasharete
- Urumqi No.1 Middle School, No. 195, West 2nd Lane, Kanas Hubei Road, Urumqi Economic and Technological Development Zone (Toutunhe District), Ürümqi, 830015, Xinjiang Uygur Autonomous Region, China
| | - Biao Luo
- Department of Orthopaedics, Pingmei Shenma Medical Group General Hospital, No.1 South of Kuanggoong Middle Road, Xinhua District, Pingdingshan, 467000, Henan, China
| | - Meihua Nihemaiti
- Altay Traditional Chinese Medicine Hospital (Regional Kazakh Medical Hospital) in Xinjiang Uygur Autonomous Region, No. 40 Yingbin Road, Altay City, 836500, Xinjiang Uygur Autonomous Region, China
| | - Jiasharete Jielile
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China.
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2
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Wientjes MG, Lu Z, Chan CHF, Turaga K, Au JLS. Surgical management of peritoneal metastasis: Opportunities for pharmaceutical research. J Control Release 2023; 361:717-726. [PMID: 37574051 PMCID: PMC10560040 DOI: 10.1016/j.jconrel.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Cytoreductive surgery (CRS) has emerged as a survival-extending treatment of peritoneal metastasis (PM); recent advances include using intraperitoneal chemotherapy (IPC) at normothermic or hyperthermic temperatures, or under pressure (CRS + IPC). Clinical CRS + IPC research has established its highly variable efficacy and suggested tumor size, tumor locations and presence of ascites as potential determinants. On the other hand, there is limited knowledge on the effects of pharmaceutical properties on treatment outcomes. The present study investigated the inter-subject variability of paclitaxel binding to proteins in patient ascites because some PM patients show accumulation of ascites and because activity and transport of highly protein-bound drugs such as paclitaxel are affected by protein binding. Ascites samples were collected from 26 patients and investigated for their protein contents using LC/MS/MS proteomics analysis and for the concentrations of total proteins and two major paclitaxel-binding proteins (human serum albumin or HSA and α-1-acid glycoprotein or AAG). The association constants of paclitaxel to HSA and AAG and the extent of protein binding of paclitaxel in patient ascites were studied using equilibrium dialysis. Proteomic analysis of four randomly selected samples revealed 288 proteins, >90% of which are also present in human plasma. Between 72% - 94% of paclitaxel was bound to proteins in patient ascites. The concentrations of HSA and AAG in ascites showed substantial inter-subject variations, ranging from 14.7 - 46.3 mg/mL and 0.13-2.56 mg/mL, respectively. The respective paclitaxel association constants to commercially available HSA and AAG were ∼ 3.5 and ∼ 120 mM. Calculation using these constants and the HSA and AAG concentrations in individual patient ascites indicated that these two proteins accounted for >85% of the total protein-binding of paclitaxel in ascites. The extensive drug binding to ascites proteins, by reducing the pharmacologically active free fraction, may lead to the diminished CRS efficacy in PM patients with ascites. Clinical advances in CRS + IPC have outpaced current knowledge of pharmaceutical properties in this setting. IPC, as a locally acting therapy, is subjected to processes different from those governing systemic treatments. This study, to our knowledge, is the first to illustrate the implications of drug properties in the CRS + IPC efficacy against PM. While drugs are now an integral part of PM patient management, there is limited pharmaceutical research in this treatment setting (e.g., effects of hyperthermia or pressure on drug transport or release from delivery systems, pharmacokinetics, pharmacodynamics). Hence, CRS + IPC of PM represents an area where additional pharmaceutical research can assist further development and optimization.
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Affiliation(s)
| | - Ze Lu
- Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, USA
| | - Carlos H F Chan
- Department of Surgery and Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Kiran Turaga
- School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Jessie L S Au
- Institute of Quantitative Systems Pharmacology, Carlsbad, CA 92008, USA; Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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3
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Lin J, Yun K, Sun Q, Xiang P, Wu L, Yang S, Dun J, Fu S, Chen H. How to sample a seizure plant: the role of the visualization spatial distribution analysis of Lophophora williamsii as an example. Forensic Sci Res 2023; 8:140-151. [PMID: 37621449 PMCID: PMC10445667 DOI: 10.1093/fsr/owad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 08/26/2023] Open
Abstract
Natural compounds in plants are often unevenly distributed, and determining the best sampling locations to obtain the most representative results is technically challenging. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide the basis for formulating sampling guideline. For a succulent plant sample, ensuring the authenticity and in situ nature of the spatial distribution analysis results during MSI analysis also needs to be thoroughly considered. In this study, we developed a well-established and reliable MALDI-MSI method based on preservation methods, slice conditions, auxiliary matrices, and MALDI parameters to detect and visualize the spatial distribution of mescaline in situ in Lophophora williamsii. The MALDI-MSI results were validated using liquid chromatography-tandem mass spectrometry. Low-temperature storage at -80°C and drying of "bookmarks" were the appropriate storage methods for succulent plant samples and their flower samples, and cutting into 40 μm thick sections at -20°C using gelatin as the embedding medium is the appropriate sectioning method. The use of DCTB (trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile) as an auxiliary matrix and a laser intensity of 45 are favourable MALDI parameter conditions for mescaline analysis. The region of interest semi-quantitative analysis revealed that mescaline is concentrated in the epidermal tissues of L. williamsii as well as in the meristematic tissues of the crown. The study findings not only help to provide a basis for determining the best sampling locations for mescaline in L. williamsii, but they also provide a reference for the optimization of storage and preparation conditions for raw plant organs before MALDI detection. Key Points An accurate in situ MSI method for fresh water-rich succulent plants was obtained based on multi-parameter comparative experiments.Spatial imaging analysis of mescaline in Lophophora williamsii was performed using the above method.Based on the above results and previous results, a sampling proposal for forensic medicine practice is tentatively proposed.
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Affiliation(s)
- Jiaman Lin
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
| | - Qiran Sun
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Ping Xiang
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Lina Wu
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Shuo Yang
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | | | - Shanlin Fu
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
| | - Hang Chen
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
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4
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Yang GM, Yan K, Wang P, Zhang JL, Pan ZH, Pan Y. ITRAQ-Based Proteomics Analysis Reveals the Effect of Neoliensinine on KCl-Induced Vascular Smooth Muscle Contraction by Inhibiting Regulatory Light Chain Phosphorylation. Front Pharmacol 2019; 10:979. [PMID: 31572175 PMCID: PMC6749048 DOI: 10.3389/fphar.2019.00979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/31/2019] [Indexed: 01/16/2023] Open
Abstract
Smooth muscle (SM) contraction is one of the important physiological functions of the human body, and SM abnormal contraction will induce many diseases. The phosphorylated regulatory light chains (p-RLC) play a decisive role in SM contraction, and dephosphorylation of p-RLC is an effective way to relax SM. Our previous study showed that the novel benzylisoquinoline alkaloid, neoliensinine (Neo), could relax microvascular SM contracted by KCl hyperpolarization. In this study, mesenteric capillaries isolated from 45 mice were divided into normal tension group (Control), 124 mM KCl induced contraction model group (Model), and KCl and Neo-treatment group (Drug). The dephosphorylation levels of RLC in the three groups were measured. Compared with the model group, the phosphorylation of RLC in the drug group was decreased dramatically as expected, suggesting that the relaxation effect of Neo was caused by downregulating p-RLC of microvessel SM. In order to fully understand its fundamental mechanism, our research focused on the identification of target proteins in mice with KCl-induced contractile mesenteric capillary. Isobaric tags for relative and absolute quantification (ITRAQ) tagging was carried out by nanospray liquid chromatography-tandem mass spectrometry. The results allowed the upregulation of 164 differential abundance proteins (DAPs) among the 3,474 protein abundance disturbances identified from the model/control samples. Further comparison showed that there were 16 DAP convergences associated with vascular SM contraction between the drug/model and the drug/control samples. Among them, two proteins with known function, PLCβ and RhoGEF12, were selected as target proteins of the relaxation effect of Neo. The two selective target DAPs were verified by Western blot at protein level. The results suggested that changes of the two proteins were consistent with that of the iTRAQ results. Our present work reveals that Neo relaxes vascular smooth muscle via inhibition of RLC phosphorylation, and PLCβ and RhoGEF12 may be potential biomarkers for evaluating the effects mediated by Neo.
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Affiliation(s)
- Guang-Ming Yang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ke Yan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peng Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun-Li Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zi-Hao Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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5
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Jin X, Lv Z, Gao J, Zhang R, Zheng T, Yin P, Li D, Peng L, Cao X, Qin Y, Persson S, Zheng B, Chen P. AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. Nucleic Acids Res 2019; 47:883-898. [PMID: 30508117 PMCID: PMC6344853 DOI: 10.1093/nar/gky1205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Modified nucleosides on tRNA are critical for decoding processes and protein translation. tRNAs can be modified through 1-methylguanosine (m1G) on position 37; a function mediated by Trm5 homologs. We show that AtTRM5a (At3g56120) is a Trm5 ortholog in Arabidopsis thaliana. AtTrm5a is localized to the nucleus and its function for m1G and m1I methylation was confirmed by mutant analysis, yeast complementation, m1G nucleoside level on single tRNA, and tRNA in vitro methylation. Arabidopsis attrm5a mutants were dwarfed and had short filaments, which led to reduced seed setting. Proteomics data indicated differences in the abundance of proteins involved in photosynthesis, ribosome biogenesis, oxidative phosphorylation and calcium signalling. Levels of phytohormone auxin and jasmonate were reduced in attrm5a mutant, as well as expression levels of genes involved in flowering, shoot apex cell fate determination, and hormone synthesis and signalling. Taken together, loss-of-function of AtTrm5a impaired m1G and m1I methylation and led to aberrant protein translation, disturbed hormone homeostasis and developmental defects in Arabidopsis plants.
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Affiliation(s)
- Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhengyi Lv
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ting Zheng
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Liangcai Peng
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xintao Cao
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Yan Qin
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville 3010, VIC, Australia.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
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6
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Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Determination of Cerebrospinal Fluid Proteome Variations by Isobaric Labeling Coupled with Strong Cation-Exchange Chromatography and Tandem Mass Spectrometry. Methods Mol Biol 2019; 2044:155-168. [PMID: 31432412 DOI: 10.1007/978-1-4939-9706-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and represents a valuable source of mediators that reflect metabolic processes occurring in the central nervous system (CNS). In this sense, mass spectrometry (MS) methods have proven to be sensitive in quantifying the proteomic profiles of CSF, therefore being able to detect biomarker candidates for neurological disorders. In particular, a key development has been the use of multiplexing technologies to easily identify and quantify complex protein mixtures. This chapter describes a workflow suitable for the analysis of CSF proteome using isobaric labeling coupled to strong cation-exchange chromatography fractionation for its potential use as a biomarker discovery platform. In this case, the isobaric tags for relative and absolute quantitation (iTRAQ) label all proteins in a sample via free amines at the N-terminus and on the side chain of lysine residues. Then, the labeled samples are pooled and chromatographically fractionated. These fractions with the pooled samples are afterward analyzed by tandem mass spectrometry (MS/MS), and proteins are quantified by the relative intensities of the reporter ions in the MS/MS spectra, simultaneously obtaining the amino acid sequence. This method complements the neuroproteomic toolbox to identify new protein biomarkers not only for the early clinical diagnosis and disease staging of CNS-related disorders but also to elucidate the molecular mechanisms related to the pathophysiology of these symptoms.
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Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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7
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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8
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Dytfeld D, Luczak M, Wrobel T, Usnarska-Zubkiewicz L, Brzezniakiewicz K, Jamroziak K, Giannopoulos K, Przybylowicz-Chalecka A, Ratajczak B, Czerwinska-Rybak J, Nowicki A, Joks M, Czechowska E, Zawartko M, Szczepaniak T, Grzasko N, Morawska M, Bochenek M, Kubicki T, Morawska M, Tusznio K, Jakubowiak A, Komarnicki MA. Comparative proteomic profiling of refractory/relapsed multiple myeloma reveals biomarkers involved in resistance to bortezomib-based therapy. Oncotarget 2018; 7:56726-56736. [PMID: 27527861 PMCID: PMC5302948 DOI: 10.18632/oncotarget.11059] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/20/2016] [Indexed: 12/17/2022] Open
Abstract
Identifying biomarkers of the resistance in multiple myeloma (MM) is a key research challenge. We aimed to identify proteins that differentiate plasma cells in patients with refractory/relapsed MM (RRMM) who achieved at least very good partial response (VGPR) and in those with reduced response to PAD chemotherapy (bortezomib, doxorubicin and dexamethasone). Comparative proteomic analysis was conducted on pretreatment plasma cells from 77 proteasome inhibitor naïve patients treated subsequently with PAD due to RRMM. To increase data confidence we used two independent proteomic platforms: isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and label free (LF). Proteins were considered as differentially expressed when their accumulation between groups differed by at least 50% in iTRAQ and LF. The proteomic signature revealed 118 proteins (35 up-regulated and 83 down-regulated in ≥ VGPR group). Proteins were classified into four classes: (1) involved in proteasome function; (2) involved in the response to oxidative stress; (3) related to defense response; and (4) regulating the apoptotic process. We confirmed the differential expression of proteasome activator complex subunit 1 (PSME1) by enzyme-linked immunosorbent assay. Increased expression of proteasomes and proteins involved in protection from oxidative stress (eg., TXN, TXNDC5) plays a major role in bortezomib resistance.
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Affiliation(s)
- Dominik Dytfeld
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.,Researchers of Polish Myeloma Consortium
| | - Magdalena Luczak
- nstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
| | - Tomasz Wrobel
- Department of Hematology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland.,Researchers of Polish Myeloma Consortium
| | - Lidia Usnarska-Zubkiewicz
- Department of Hematology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Brzezniakiewicz
- Department of Hematology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland.,Researchers of Polish Myeloma Consortium
| | - Krzysztof Jamroziak
- Institute of Hematology and Transfusiology, Warsaw, Poland.,Researchers of Polish Myeloma Consortium
| | - Krzysztof Giannopoulos
- Experimental Hematooncology Department, Medical University of Lublin and Hematology Department, St John's Cancer Center in Lublin, Lublin, Poland.,Researchers of Polish Myeloma Consortium
| | - Anna Przybylowicz-Chalecka
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Blazej Ratajczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Czerwinska-Rybak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Adam Nowicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.,Researchers of Polish Myeloma Consortium
| | - Monika Joks
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.,Researchers of Polish Myeloma Consortium
| | - Elzbieta Czechowska
- Department of Internal Medicine and Hematology, StanisÅaw Staszic Specialist Hospital, PiÅa, Poland.,Researchers of Polish Myeloma Consortium
| | | | - Tomasz Szczepaniak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.,Researchers of Polish Myeloma Consortium
| | - Norbert Grzasko
- Experimental Hematooncology Department, Medical University of Lublin and Hematology Department, St John's Cancer Center in Lublin, Lublin, Poland.,Researchers of Polish Myeloma Consortium
| | - Marta Morawska
- Experimental Hematooncology Department, Medical University of Lublin and Hematology Department, St John's Cancer Center in Lublin, Lublin, Poland.,Researchers of Polish Myeloma Consortium
| | - Maciej Bochenek
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Tadeusz Kubicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Michalina Morawska
- Department of Hematology, Hospital in Gorzow Wlkp, Gorzow Wlkp, Poland.,Researchers of Polish Myeloma Consortium
| | | | | | - MieczysÅ Aw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
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9
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Hooshmand S, Es'haghi Z. Hydrophilic modified magnetic multi-walled carbon nanotube for dispersive solid/liquid phase microextraction of sunitinib in human samples. Anal Biochem 2018; 542:76-83. [DOI: 10.1016/j.ab.2017.11.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 12/26/2022]
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10
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Luczak M, Formanowicz D, Marczak Ł, Suszyńska-Zajczyk J, Pawliczak E, Wanic-Kossowska M, Stobiecki M. iTRAQ-based proteomic analysis of plasma reveals abnormalities in lipid metabolism proteins in chronic kidney disease-related atherosclerosis. Sci Rep 2016; 6:32511. [PMID: 27600335 PMCID: PMC5013279 DOI: 10.1038/srep32511] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022] Open
Abstract
Patients with chronic kidney disease (CKD) have a considerably higher risk of death due to cardiovascular causes. Using an iTRAQ MS/MS approach, we investigated the alterations in plasma protein accumulation in patients with CKD and classical cardiovascular disease (CVD) without CKD. The proteomic analysis led to the identification of 130 differentially expressed proteins among CVD and CKD patients and healthy volunteers. Bioinformatics analysis revealed that 29 differentially expressed proteins were involved in lipid metabolism and atherosclerosis, 20 of which were apolipoproteins and constituents of high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Although dyslipidemia is common in CKD patients, we found that significant changes in apolipoproteins were not strictly associated with changes in plasma lipid levels. A lack of correlation between apoB and LDL concentration and an inverse relationship of some proteins with the HDL level were revealed. An increased level of apolipoprotein AIV, adiponectin, or apolipoprotein C, despite their anti-atherogenic properties, was not associated with a decrease in cardiovascular event risk in CKD patients. The presence of the distinctive pattern of apolipoproteins demonstrated in this study may suggest that lipid abnormalities in CKD are characterized by more qualitative abnormalities and may be related to HDL function rather than HDL deficiency.
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Affiliation(s)
- Magdalena Luczak
- European Centre for Bioinformatics and Genomics, Institute of
Bioorganic Chemistry, Poznan, 61-138,
Poland
- Institute of Chemical Technology and Engineering, Poznan
University of Technology, Poznan, 60-965,
Poland
| | - Dorota Formanowicz
- Department of Clinical Biochemistry and Laboratory Medicine,
Poznan University of Medical Sciences, Poznan,
60-780, Poland
| | - Łukasz Marczak
- European Centre for Bioinformatics and Genomics, Institute of
Bioorganic Chemistry, Poznan, 61-138,
Poland
| | - Joanna Suszyńska-Zajczyk
- Department of Biochemistry and Biotechnology, Poznan University
of Life Sciences, Poznan, 60-632,
Poland
| | - Elżbieta Pawliczak
- Department of Nephrology, Transplantology and Internal Medicine,
Poznan University of Medical Sciences, Poznan,
60-355, Poland
| | - Maria Wanic-Kossowska
- Department of Nephrology, Transplantology and Internal Medicine,
Poznan University of Medical Sciences, Poznan,
60-355, Poland
| | - Maciej Stobiecki
- European Centre for Bioinformatics and Genomics, Institute of
Bioorganic Chemistry, Poznan, 61-138,
Poland
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11
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Luczak M, Suszynska-Zajczyk J, Marczak L, Formanowicz D, Pawliczak E, Wanic-Kossowska M, Stobiecki M. Label-Free Quantitative Proteomics Reveals Differences in Molecular Mechanism of Atherosclerosis Related and Non-Related to Chronic Kidney Disease. Int J Mol Sci 2016; 17:E631. [PMID: 27144566 PMCID: PMC4881457 DOI: 10.3390/ijms17050631] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 11/16/2022] Open
Abstract
The major cause of mortality in patients with chronic kidney disease (CKD) is atherosclerosis related to traditional and non-traditional risk factors. However, the understanding of the molecular specificity that distinguishes the risk factors for classical cardiovascular disease (CVD) and CKD-related atherosclerosis (CKD-A) is far from complete. In this study we investigated the disease-related differences in the proteomes of patients with atherosclerosis related and non-related to CKD. Plasma collected from patients in various stages of CKD, CVD patients without symptoms of kidney dysfunction, and healthy volunteers (HVs), were analyzed by a coupled label-free and mass spectrometry approach. Dysregulated proteins were confirmed by an enzyme-linked immunosorbent assay (ELISA). All proteomic data were correlated with kidney disease development and were subjected to bioinformatics analysis. One hundred sixty-two differentially expressed proteins were identified. By directly comparing the plasma proteomes from HVs, CKD, and CVD patients in one study, we demonstrated that proteins involved in inflammation, blood coagulation, oxidative stress, vascular damage, and calcification process exhibited greater alterations in patients with atherosclerosis related with CKD. These data indicate that the above nontraditional risk factors are strongly specific for CKD-A and appear to be less essential for the development of "classical" CVD.
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Affiliation(s)
- Magdalena Luczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland.
| | - Joanna Suszynska-Zajczyk
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Lukasz Marczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Dorota Formanowicz
- Department of Clinical Biochemistry and Laboratory Medicine, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland.
| | - Elzbieta Pawliczak
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznan, Poland.
| | - Maria Wanic-Kossowska
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznan, Poland.
| | - Maciej Stobiecki
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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12
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Wei H, Ma Y, Liu J, Ding C, Hu F, Yu L. Proteomic analysis of cortical brain tissue from the BTBR mouse model of autism: Evidence for changes in STOP and myelin-related proteins. Neuroscience 2016; 312:26-34. [DOI: 10.1016/j.neuroscience.2015.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 01/19/2023]
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13
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Pantham P, Viall CA, Chen Q, Kleffmann T, Print CG, Chamley LW. Antiphospholipid antibodies bind syncytiotrophoblast mitochondria and alter the proteome of extruded syncytial nuclear aggregates. Placenta 2015; 36:1463-73. [PMID: 26506561 DOI: 10.1016/j.placenta.2015.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/28/2015] [Accepted: 10/11/2015] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Antiphospholipid antibodies (aPL) are autoantibodies that increase the risk of women developing the hypertensive disorder pre-eclampsia. aPL are internalised by the syncytiotrophoblast and increase extrusion of necrotic multinucleated syncytial nuclear aggregates (SNAs), which may trigger endothelial dysfunction in pre-eclampsia. The mechanisms by which aPL alter death processes in the syncytiotrophoblast leading to extrusion of SNAs are unknown. METHODS First trimester human placentae (n = 10) were dissected into explants and cultured either with aPL (50 μg/mL), isotype-matched control antibody (50 μg/mL), or media for 24 h. Harvested SNAs underwent iTRAQ proteomic analysis. Mitochondria in syncytiotrophoblast treated with aPL labelled with FluoroNanogold were visualised using transmission electron microscopy (TEM). RESULTS aPL altered the expression of 72 proteins in SNAs. Thirteen proteins were involved in mitochondrial function. TEM demonstrated that aPL bind to mitochondria in the syncytiotrophoblast and may cause mitochondrial swelling. DISCUSSION aPL disrupt mitochondria increasing the extrusion of SNAs with an altered proteome from the syncytiotrophoblast. These altered SNAs may trigger endothelial dysfunction and pre-eclampsia in these pregnancies.
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Affiliation(s)
- Priyadarshini Pantham
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand; Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Chez A Viall
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Qi Chen
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand; Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
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14
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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15
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Luczak M, Formanowicz D, Marczak Ł, Pawliczak E, Wanic-Kossowska M, Figlerowicz M, Stobiecki M. Deeper insight into chronic kidney disease-related atherosclerosis: comparative proteomic studies of blood plasma using 2DE and mass spectrometry. J Transl Med 2015; 13:20. [PMID: 25622820 PMCID: PMC4316657 DOI: 10.1186/s12967-014-0378-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/30/2014] [Indexed: 12/17/2022] Open
Abstract
Background Atherosclerosis is a major cause of cardiac events and mortality in patients suffering from chronic kidney disease (CKD). Moreover, the risk of cardiovascular disease (CVD) development in patients with CKD increases as kidney function declines. Although the close connection between atherosclerosis and kidney dysfunction is undeniable, particular risk factors and specific mechanisms that promote CVD in patients with CKD remain unclear. To gain insight into better recognition of the mechanisms of accelerated atherosclerosis in patients with CKD, we performed a comparative proteomic analysis of blood plasma from patients in various stages of CKD and thus distinct progression of atherosclerosis (n = 90), patients with advanced CVD and normal renal function (n = 30) and healthy volunteers (n = 30). Methods Plasma samples were depleted using affinity chromatography and divided into three fractions: high-abundant, low-abundant and low-molecular weight proteins. The first two fractions were analyzed by two-dimensional gel electrophoresis and mass spectrometry, the last one has been subjected to direct MS/MS analysis. A proteomic profiles for high-abundant, low-abundant and low-molecular weight proteins fractions were obtained. Differential accumulated proteins were confirmed by selected reaction monitoring analysis (SRM). The Gene Ontology (GO) function and the interaction networks of differentially expressed proteins were then analyzed. Results Forty-nine proteins (13 high- and 36 low-molecular mass) showed differences in accumulation levels. For eleven of them differential expression were confirmed by selected reaction monitoring analysis. Bioinformatic analysis showed that identified differential proteins were related to three different processes: the blood coagulation cascade, the transport, binding and metabolism of lipoproteins and inflammatory processes. Conclusions Obtained data provide an additional line of evidence that different molecular mechanisms are involved in the development of CKD- and CVD-related atherosclerosis. The abundance of some anti-atherogenic factors revealed in patients with CKD suggests that these factors are not associated with the reduction of atherosclerosis progression in CKD that is typically observed in “classical” CVD. Moreover, obtained data also suggest that mechanism of CVD acceleration may be different in initial and advanced stages of CKD. Undoubtedly, in advanced stages of CKD inflammation is highly pronounced. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0378-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Chemical Technology and Engineering, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland.
| | - Dorota Formanowicz
- Department of Clinical Biochemistry, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780, Poznan, Poland.
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Elżbieta Pawliczak
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland.
| | - Maria Wanic-Kossowska
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Maciej Stobiecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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