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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system, particularly in the separation of intact proteins. A modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual protein species including protein isoforms and post-translational modifications. This chapter discusses the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research, particularly on recombinant Chinese hamster ovary cells, which are also discussed in this chapter.
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Affiliation(s)
- Paula Meleady
- School of Biotechnology, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.
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Zhang X, Yu W, Cao X, Wang Y, Zhu C, Guan J. Identification of Serum Biomarkers in Patients with Alzheimer's Disease by 2D-DIGE Proteomics. Gerontology 2022; 68:686-698. [PMID: 35021178 DOI: 10.1159/000520961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/09/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
AIM The aim of this study is to identify potential serum biomarkers of Alzheimer's disease (AD) for early diagnosis and to evaluate these markers on a large cohort. METHODS We performed two-dimensional difference gel electrophoresis to compare the serum of AD patients and normal controls. Western blot or enzyme-linked immunosorbent assay (ELISA) was used to identify the expression levels of proteins. RESULTS In this study, a total of 13 differentially expressed proteins were identified. Among them, 2 proteins (inter-alpha-trypsin inhibitor heavy chain H4 [ITI-H4], Apolipoprotein A-IV) were validated by Western blot and 4 proteins (Cofilin 2, Tetranectin, Zinc-alpha-2-glycoprotein [AZGP1], Alpha-1-microglobulin/bikunin precursor [AMBP]) were validated by ELISA, respectively. Western blot results showed that the full size of the ITI-H4 protein was increased, while a fragment of ITI-H4 was decreased in AD patients. In contrast, 1 fragment of Apo A-IV was mainly found in control group and rare to be detected in AD patients. On the other hand, ELISA results showed that Cofilin 2, Tetranectin, AZGP1, and AMBP were significantly increased in AD patients, and Cofilin 2 is strongly correlated with the Mini-Mental State Examination scores of the AD patients. Serum Cofilin 2 was unchanged in Parkinson disease patients as compared to the control group, indicating a specific correlation of serum Cofilin 2 with AD. Moreover, Cofilin 2 was increased in both the serum and brain tissue in the APP/PS1 transgenic mice. CONCLUSION Our study identified several potential serum biomarkers of AD, including: ITI-H4, ApoA-IV, Cofilin 2, Tetranectin, AZGP1, and AMBP. Cofilin 2 was upregulated in different AD animal models and might play important roles in AD pathology.
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Affiliation(s)
- Xuezhi Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenwen Yu
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao, China
| | - Xuelei Cao
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yongbin Wang
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chao Zhu
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jialiang Guan
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
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Li Z, Shen H, Liu Y, Zhou X, Yan M, He H, Zhao T, Zhang H, Li P. Subproteomic profiling from renal cortices in OLETF rats reveals mutations of multiple novel genes in diabetic nephropathy. Genes Genomics 2021; 44:109-122. [PMID: 34643893 DOI: 10.1007/s13258-021-01174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/19/2020] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Diabetic nephropathy (DN) is a serious threat to human health, but its pathogenesis is not fully understood. Otsuka Long-Evans Tokushima Fatty (OLETF) rats are very similar to human DN in many aspects such as pathological changes and processes, and are deemed to be an ideal rodent model. OBJECTIVE This study was aimed to explore the pathogenesis of DN by analyzing the protein expression profile from renal cortices in OLETF rats. METHODS Thirty-six-week-old diabetic OLETF rats and normal control Long-Evans Tokushima Otsuka (LETO) rats were nephrectomized, and the renal cortices were isolated. The proteins were separated by soluble and insoluble high-resolution subproteomics methods for the analysis and identification of differential proteins. RESULTS Thirty-six differentially expressed proteins were found. Among them, 11 proteins had different isoelectric points and molecular weights between OLETF and LETO rats. Further sequencing identified point mutations in genes encoding eight of these proteins, which are involved in many biological processes closely related to DN, including oxidative stress and inflammation. Five of these eight proteins have not been reported in DN. CONCLUSION This study reveals mutations of multiple novel genes in diabetic OLETF rats, providing some new potential targets for the pathogenesis of DN and helping to better understand the pathogenesis of DN.
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Affiliation(s)
- Zhiguo Li
- Department of School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for chronic disease, North China University of Science and Technology, Tangshan, 063000, China
| | - Hong Shen
- Department of Modern Technology and Education, North China University of Science and Technology, Tangshan, 063000, China
| | - Yeqiang Liu
- Department of Endocrinology, Kailuan General Hospital, North China University of Science and Technology, Tangshan, 063000, China
| | - Xuefeng Zhou
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, 2 Yinghua East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Meihua Yan
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, 2 Yinghua East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Hailan He
- School of Graduate Studies, North China University of Science and Technology, Tangshan, 063000, China
| | - Tingting Zhao
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, 2 Yinghua East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Haojun Zhang
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, 2 Yinghua East Road, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Ping Li
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, 2 Yinghua East Road, Chaoyang District, Beijing, 100029, People's Republic of China.
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Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) remains to be one of the most popular and versatile methods of protein separation among many proteomics technologies. Similar to traditional two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the proteins are separated based on their charges and molecular weight by 2D-DIGE. Different from 2D-PAGE, proteins are pre-labeled with different fluorescent dyes, and different protein samples are run in one gel by this method. Therefore, 2D-DIGE not only carries the advantages of 2D-PAGE but also eliminates gel-to-gel variation and achieves high resolution, sensitivity, and reproducibility.
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Mohanty G, Jena SR, Nayak J, Kar S, Samanta L. Proteomic Signatures in Spermatozoa Reveal the Role of Paternal Factors in Recurrent Pregnancy Loss. World J Mens Health 2019; 38:103-114. [PMID: 31385471 PMCID: PMC6920069 DOI: 10.5534/wjmh.190034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/18/2019] [Accepted: 05/18/2019] [Indexed: 12/17/2022] Open
Abstract
Purpose To identify the paternal factors responsible for aberrant embryo development leading to loss of foetus in recurrent pregnancy loss (RPL) through proteomic analysis of ejaculated spermatozoa. Materials and Methods This prospective study consisted of male partners of RPL patients (n=16) experienced with two or more consecutive unexplained miscarriages and with no female factor abnormality as revealed by gynaecologic investigation including karyotyping and age matched fertile healthy volunteers (n=20). All samples were collected during 2013 to 2015 after getting institutional ethical approval and written consent from the participants. Seminal ejaculates were collected by masturbation after 2 to 3 days of sexual abstinence and analyzed according to World Health Organization 5th criteria 2010. Two-dimensional difference gel electrophoresis followed by mass spectrophotometric analysis was used to identify differentially expressed proteins (DEPs). Western blotting was used for validation of the key proteins. Results The data identified 36 protein spots to be differentially expressed by more than 2-fold change with p<0.05 considered as significant. Matrix-assisted laser desorption/ionization time of flight/mass spectrometry identified GPx4, JIP4, ZN248 to be overexpressed while HSPA2, GSTM5, TF3C1, CC74A was underexpressed in RPL group. Western blot analysis confirmed the differential expression of key redox associated proteins GPx4 and HSPA2 in the RPL group. Functional analysis revealed the involvement of key biological processes that includes spermatogenesis, response to oxidative stress, protein folding and metabolic process. Conclusions The present study provides a snapshot of the altered protein expression levels consistent with the potential involvement of the sperm chromatin landscape in early embryonic development.
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Affiliation(s)
- Gayatri Mohanty
- Redox Biology Laboratory, Department of Zoology, Center of Excellence in Environment and Public Health, Ravenshaw University, Cuttack, India
| | - Soumya Ranjan Jena
- Redox Biology Laboratory, Department of Zoology, Center of Excellence in Environment and Public Health, Ravenshaw University, Cuttack, India
| | - Jasmine Nayak
- Redox Biology Laboratory, Department of Zoology, Center of Excellence in Environment and Public Health, Ravenshaw University, Cuttack, India
| | - Sujata Kar
- Department of Obstetrics and Gynaecology, Kar Clinic and Hospital Private Limited, Bhubaneswar, India
| | - Luna Samanta
- Redox Biology Laboratory, Department of Zoology, Center of Excellence in Environment and Public Health, Ravenshaw University, Cuttack, India.
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Kondo T. Cancer biomarker development and two-dimensional difference gel electrophoresis (2D-DIGE). Biochim Biophys Acta Proteins Proteom 2018; 1867:2-8. [PMID: 30392560 DOI: 10.1016/j.bbapap.2018.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 02/08/2023]
Abstract
Cancer results from the accumulation of genomic alterations. As the genome is functionally translated to the proteome and regulates tumor cell behavior, proteomics studies are expected to further the current understanding of the molecular mechanisms underlying carcinogenesis and cancer progression. Biomarkers are potential tools to classify cancers for therapy, predict responses to treatments, and support treatment-related decision-making. Biomarker development has been actively pursued in oncology by proteomic approaches. Two-dimensional difference gel electrophoresis (2D-DIGE) is a proteomics technique based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). In 2D-DIGE, protein samples are labeled with distinct fluorescent dyes before fractionation via 2D-PAGE. 2D-DIGE offers advantages to identify biomarker candidates, including reproducibility, high sensitivity, comprehensiveness, and high throughput. 2D-DIGE has contributed to the establishment of tissue biomarkers, which potentially facilitate precision medicine. 2D-DIGE is thus expected to yield major advancements in cancer biomarker identification and development.
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Affiliation(s)
- Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Japan.
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Xu DD, Xu CB, Lam HM, Wong FL, Leung AWN, Leong MML, Cho WCS, Hoeven R, Lv Q, Rong R. Proteomic analysis reveals that pheophorbide a-mediated photodynamic treatment inhibits prostate cancer growth by hampering GDP-GTP exchange of ras-family proteins. Photodiagnosis Photodyn Ther 2018; 23:35-39. [PMID: 29800714 DOI: 10.1016/j.pdpdt.2018.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND We previously reported that pheophorbide a (PhA), excited by 630 nm light, significantly inhibited the growth of prostate cancer cells. In this study, we employed whole-cell proteomics to investigate photodynamic treatment (PDT)-related proteins. METHODS Two-dimensional gel electrophoresis (2-DE) coupled with tandem mass spectrometry was employed to reveal the proteins involved in PhA-mediated PDT in LNCaP and PC-3 prostate cancer cells. RESULTS After PhA-PDT treatment, decreased expression of translationally-controlled tumor protein (TCTP) was found in both PC-3 and LNCaP whole-cell proteomes. In contrast, human rab GDP dissociation inhibitor (GDI) in LNCaP cells and ras-related homologs GDI in PC-3 cells were up-regulated. CONCLUSIONS GDP-GTP exchange is an underlying target of photodynamic treatment in prostate cancer cells.
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Affiliation(s)
- Dan Dan Xu
- Shandong University of Traditional Chinese Medicine, Jinan, China.
| | - Chong Bing Xu
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, China
| | - Hon Ming Lam
- School of Life Science, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Fuk-Ling Wong
- School of Life Science, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | | | - Merrin Man Long Leong
- Department of Clinical Oncology, University of Hong Kong, Hong Kong Special Administrative Region
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region
| | - Robin Hoeven
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Qingtao Lv
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Rong Rong
- Shandong University of Traditional Chinese Medicine, Jinan, China.
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual proteins species including protein isoforms and post-translational modifications. This review will discuss the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research (particularly on recombinant Chinese hamster ovary cells), which will also be discussed in the review chapter.
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Affiliation(s)
- Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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Kikuta K, Kubota D, Yoshida A, Qiao Z, Morioka H, Nakamura M, Matsumoto M, Chuman H, Kawai A, Kondo T. Discoidin, CUB and LCCL domain-containing protein 2 (DCBLD2) is a novel biomarker of myxofibrosarcoma invasion identified by global protein expression profiling. Biochim Biophys Acta Proteins Proteom 2017; 1865:1160-1166. [PMID: 28668639 DOI: 10.1016/j.bbapap.2017.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/24/2017] [Indexed: 12/20/2022]
Abstract
Myxofibrosarcoma (MFS) is a mesenchymal malignancy characterized by frequent recurrence even after radical wide resection. To optimize therapy for MFS patients, we aimed to identify candidate tissue biomarkers of MFS invasion potential. Invasion characteristics of MFS were evaluated by magnetic resonance imaging and protein expression profiling of primary tumor tissues performed using two-dimensional difference gel electrophoresis (2D-DIGE). Protein expression profiles were compared between invasive and non-invasive tumors surgically resected from 11 patients. Among the 3453 protein spots observed, 59 demonstrated statistically significant difference in intensity (≥2-fold) between invasive and non-invasive tumors (p<0.01 by Wilkoxon test), and were identified by mass spectrometry as 47 individual proteins. Among them, we further focused on discoidin, CUB and LCCL domain-containing protein 2 (DCBLD2), a receptor tyrosine kinase with aberrant expression in malignant tumors. Immunohistochemistry analysis of 21 additional MFS cases revealed that higher DCBLD2 expression was significantly associated with invasive properties of tumor cells. DCBLD2 sensitivity and specificity, and positive and negative predictive values for MFS invasion were 69.2%, 87.5%, 90%, and 63.6%, respectively. The expression level of DCBLD2 was consistent in different portions of tumor tissues. Thus, DCBLD2 expression can be a useful biomarker to evaluate invasive properties of MFS. Further validation studies based on multi-institutional collaboration and comprehensive analysis of DCBLD2 biological functions in MFS are required to confirm its prognostic utility for clinical application.
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Affiliation(s)
- Kazutaka Kikuta
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; Department of Orthopedic Surgery, Keio University School of Medicine, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Daisuke Kubota
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Akihiko Yoshida
- Pathology and Clinical Laboratory Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Zhiwei Qiao
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hideo Morioka
- Department of Orthopedic Surgery, Keio University School of Medicine, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopedic Surgery, Keio University School of Medicine, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hirokazu Chuman
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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Katrinli S, Ozdil K, Sahin A, Ozturk O, Kir G, Baykal AT, Akgun E, Sarac OS, Sokmen M, Doğanay HL, Dinler Doğanay G. Proteomic profiling of HBV infected liver biopsies with different fibrotic stages. Proteome Sci 2017; 15:7. [PMID: 28439208 PMCID: PMC5399407 DOI: 10.1186/s12953-017-0114-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/05/2017] [Indexed: 12/13/2022] Open
Abstract
Background Hepatitis B virus (HBV) is a global health problem, and infected patients if left untreated may develop cirrhosis and eventually hepatocellular carcinoma. This study aims to enlighten pathways associated with HBV related liver fibrosis for delineation of potential new therapeutic targets and biomarkers. Methods Tissue samples from 47 HBV infected patients with different fibrotic stages (F1 to F6) were enrolled for 2D-DIGE proteomic screening. Differentially expressed proteins were identified by mass spectrometry and verified by western blotting. Functional proteomic associations were analyzed by EnrichNet application. Results Fibrotic stage variations were observed for apolipoprotein A1 (APOA1), pyruvate kinase PKM (KPYM), glyceraldehyde 3-phospahate dehydrogenase (GAPDH), glutamate dehydrogenase (DHE3), aldehyde dehydrogenase (ALDH2), alcohol dehydrogenase (ALDH1A1), transferrin (TRFE), peroxiredoxin 3 (PRDX3), phenazine biosynthesis-like domain-containing protein (PBLD), immuglobulin kappa chain C region (IGKC), annexin A4 (ANXA4), keratin 5 (KRT5). Enrichment analysis with Reactome and Kegg databases highlighted the possible involvement of platelet release, glycolysis and HDL mediated lipid transport pathways. Moreover, string analysis revealed that HIF-1α (Hypoxia-inducible factor 1-alpha), one of the interacting partners of HBx (Hepatitis B X protein), may play a role in the altered glycolytic response and oxidative stress observed in liver fibrosis. Conclusions To our knowledge, this is the first protomic research that studies HBV infected fibrotic human liver tissues to investigate alterations in protein levels and affected pathways among different fibrotic stages. Observed changes in the glycolytic pathway caused by HBx presence and therefore its interactions with HIF-1α can be a target pathway for novel therapeutic purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12953-017-0114-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seyma Katrinli
- Molecular Biology Biotechnology and Genetics Research Center (MOBGAM), Istanbul Technical University, Sariyer, Istanbul, Turkey
| | - Kamil Ozdil
- Gastroenterology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - Abdurrahman Sahin
- Gastroenterology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - Oguzhan Ozturk
- Gastroenterology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - Gozde Kir
- Pathology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem University, Istanbul, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry, School of Medicine, Acibadem University, Istanbul, Turkey
| | - Omer Sinan Sarac
- Computer Engineering, Istanbul Technical University, Sarıyer, Istanbul, Turkey
| | - Mehmet Sokmen
- Gastroenterology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - H Levent Doğanay
- Gastroenterology, Umraniye Teaching and Research Hospital, Umraniye, Istanbul, Turkey
| | - Gizem Dinler Doğanay
- Molecular Biology Biotechnology and Genetics Research Center (MOBGAM), Istanbul Technical University, Sariyer, Istanbul, Turkey
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Chen YB, Wang D, Ge XL, Zhao BG, Wang XC, Wang BC. Comparative proteomics of leaves found at different stem positions of maize seedlings. J Plant Physiol 2016; 198:116-28. [PMID: 27176136 DOI: 10.1016/j.jplph.2016.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/26/2016] [Accepted: 03/30/2016] [Indexed: 05/11/2023]
Abstract
To better understand the roles of leaves at different stem positions during plant development, we measured the physiological properties of leaves 1-4 on maize seedling stems, and performed a proteomics study to investigate the differences in protein expression in the four leaves using two-dimensional difference gel electrophoresis and tandem mass spectrometry in conjunction with database searching. A total of 167 significantly differentially expressed protein spots were found and identified. Of these, 35% are involved in photosynthesis. By further analysis of the data, we speculated that in leaf 1 the seedling has started to transition from a heterotroph to an autotroph, development of leaf 2 is the time at which the seedling fully transitions from a heterotroph to an autotroph, and leaf maturity was reached only with fully expanded leaves 3 and 4, although there were still some protein expression differences in the two leaves. These results suggest that the different leaves make different contributions to maize seedling growth via modulation of the expression of the photosynthetic proteins. Together, these results provide insight into the roles of the different maize leaves as the plant develops from a heterotroph to an autotroph.
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Affiliation(s)
- Yi-Bo Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Dan Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Xuan-Liang Ge
- Institute of Cultivation and Tillage of Heilongjiang Academy of Agricultural Sciences, Haerbin, Heilongjiang, China
| | - Biligen-Gaowa Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Xu-Chu Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China.
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Cooney JM, Barnett MPG, Dommels YEM, Brewster D, Butts CA, McNabb WC, Laing WA, Roy NC. A combined omics approach to evaluate the effects of dietary curcumin on colon inflammation in the Mdr1a(-/-) mouse model of inflammatory bowel disease. J Nutr Biochem 2015; 27:181-92. [PMID: 26437580 DOI: 10.1016/j.jnutbio.2015.08.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 12/12/2014] [Revised: 08/04/2015] [Accepted: 08/27/2015] [Indexed: 12/15/2022]
Abstract
The aim of this study was to provide insight into how curcumin reduces colon inflammation in the Mdr1a(-/-) mouse model of human inflammatory bowel disease using a combined transcriptomics and proteomics approach. Mdr1a(-/-) and FVB control mice were randomly assigned to an AIN-76A (control) diet or AIN-76A+0.2% curcumin. At 21 or 24weeks of age, colonic histological injury score (HIS) was determined, colon mRNA transcript levels were assessed using microarrays and colon protein expression was measured using 2D gel electrophoresis and LCMS protein identification. Colonic HIS of Mdr1a(-/-) mice fed the AIN-76A diet was higher (P<.001) than FVB mice fed the same diet; the curcumin-supplemented diet reduced colonic HIS (P<.05) in Mdr1a(-/-) mice. Microarray and proteomics analyses combined with new data analysis tools, such as the Ingenuity Pathways Analysis regulator effects analysis, showed that curcumin's antiinflammatory activity in Mdr1a(-/-) mouse colon may be mediated by activation of α-catenin, which has not previously been reported. We also show evidence to support curcumin's action via multiple molecular pathways including reduced immune response, increased xenobiotic metabolism, resolution of inflammation through decreased neutrophil migration and increased barrier remodeling. Key transcription factors and other regulatory molecules (ERK, FN1, TNFSF12 and PI3K complex) activated in inflammation were down-regulated by dietary intervention with curcumin.
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Affiliation(s)
- Janine M Cooney
- Biological Chemistry & Bioactives Group and Food Innovation, Plant & Food Research, Hamilton 3240, New Zealand
| | - Matthew P G Barnett
- Food Nutrition & Health Team, Food & Bio-based Products Group, Palmerston North 4442, New Zealand; GRAVIDA: National Centre for Growth and Development, Auckland 1142, New Zealand.
| | - Yvonne E M Dommels
- Food and Nutrition, Food Innovation, Plant & Food Research, Palmerston North 4442, New Zealand
| | - Diane Brewster
- Biological Chemistry & Bioactives Group and Food Innovation, Plant & Food Research, Auckland 1025, New Zealand
| | - Christine A Butts
- Food and Nutrition, Food Innovation, Plant & Food Research, Palmerston North 4442, New Zealand
| | - Warren C McNabb
- AgResearch, Palmerston North 4442, New Zealand; Riddet Institute, Massey University, Palmerston North 4474, New Zealand
| | - William A Laing
- Biological Chemistry & Bioactives Group and Food Innovation, Plant & Food Research, Auckland 1025, New Zealand
| | - Nicole C Roy
- Food Nutrition & Health Team, Food & Bio-based Products Group, Palmerston North 4442, New Zealand; GRAVIDA: National Centre for Growth and Development, Auckland 1142, New Zealand; Riddet Institute, Massey University, Palmerston North 4474, New Zealand
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Mimae T, Ito A. New challenges in pseudopodial proteomics by a laser-assisted cell etching technique. Biochim Biophys Acta 2014; 1854:538-46. [PMID: 25461796 DOI: 10.1016/j.bbapap.2014.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/10/2014] [Accepted: 10/10/2014] [Indexed: 12/26/2022]
Abstract
Pseudopodia are ventral membrane protrusions that extend toward higher concentrations of chemoattractants and play key roles in cell migration and cancer cell invasion. Cancers, including carcinoma and sarcoma, become life threatening when they invade surrounding structures and other organs. Understanding the molecular basis of invasiveness is important for the elimination of cancers. Thus, determining the pseudopodial composition will offer insights into the mechanisms underlying tumor cell invasiveness and provide potential biomarkers and therapeutic targets. Pseudopodial composition has been extensively investigated by using proteomic approaches. A variety of modalities, including gel-based and mass spectrometry-based methods, have been employed for pseudopodial proteomics. Our research group recently established a novel method using excimer laser pulses to selectively harvest pseudopodia, and we successfully identified a number of new pseudopodial constituents. Here, we summarized the conventional proteomic procedures and describe our new excimer laser-assisted method, with a special emphasis on the differences in the methods used to isolate pseudopodia. In addition, we discussed the theoretical background for the use of excimer laser-mediated cell ablation in proteomic applications. Using the excimer laser-assisted method, we showed that alpha-parvin, an actin-binding adaptor protein, is localized to pseudopodia, and is involved in breast cancer invasiveness. Our results clearly indicate that excimer laser-assisted cell etching is a useful technique for pseudopodial proteomics. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Takahiro Mimae
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8551, Japan.
| | - Akihiko Ito
- Department of Pathology, Faculty of Medicine, Kinki University, Osaka 589-8511, Japan
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Hu X, Zhang H, Zhang Y, Zhang Y, Bai L, Chen Q, Wu J, Zhang L. Differential protein profile of PC12 cells exposed to proteasomal inhibitor lactacystin. Neurosci Lett 2014; 575:25-30. [PMID: 24858133 DOI: 10.1016/j.neulet.2014.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 07/06/2013] [Revised: 04/09/2014] [Accepted: 05/13/2014] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide and recent studies implicate a central role for ubiquitin-proteasome system (UPS) impairment in the etiopathogenesis of PD. To explore the possible role of UPS dysfunction in PD and the proteins involved, PC12 cells were treated with 10μM lactacystin, a 20S proteasome inhibitor, for 24h. Lactacystin induced cell death and α-synuclein-positive inclusions in cytoplasm. Following two-dimensional difference in-gel electrophoresis (2-D DIGE) which was used to separate the cellular proteins, the proteins that were significantly altered were analyzed and identified. Proteomic study identified 6 differentially expressed proteins between lactacystin-treated and control cells in this study. Four proteins (heat shock 70kDa protein 8, 78kDa glucose-regulated protein, serine proteinase inhibitor clade B member 6 and aldehyde reductase) were increased and 2 proteins (peripherin and tyrosine hydroxylase) were decreased following proteasomal inhibition. The results revealed that PC12 cells treated with 10μM lactacystin for 24h could be used as a cellular model of PD. The proteins identified in the present indicate not only the damage of proteasomal inhibition to the cells but also the possible responses of the cells. These data show that proteomic study may provide information relevant to biological basis for PD and potential new treatment targets.
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Affiliation(s)
- Xinyu Hu
- Department of Neurology, The First Hospital, Jilin University, Changchun 130021, China
| | - Haina Zhang
- Department of Rehabilitation, The Second Hospital, Jilin University, Changchun 130041, China
| | - Yizhi Zhang
- Department of Neurology, The Second Hospital, Jilin University, Changchun 130041, China
| | - Ying Zhang
- Department of Neurology, The Second Hospital, Jilin University, Changchun 130041, China
| | - Ling Bai
- Department of Clinical Medicine, Norman Bethune Health Science Center, Jilin University, Changchun 130021, China
| | - Qiuhui Chen
- Department of Neurology, The Second Hospital, Jilin University, Changchun 130041, China
| | - Jiang Wu
- Department of Neurology, The First Hospital, Jilin University, Changchun 130021, China
| | - Lei Zhang
- Department of Pediatrics, The Second Hospital, Jilin University, Changchun 130041, China.
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