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Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis. Adv Virus Res 2020; 109:201-254. [PMID: 33934828 DOI: 10.1016/bs.aivir.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The DNA viruses, Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), are members of the gammaherpesvirus subfamily, a group of viruses whose infection is associated with multiple malignancies, including cancer. The primary host for these viruses is humans and, like all herpesviruses, infection with these pathogens is lifelong. Due to the persistence of gammaherpesvirus infection and the potential for cancer formation in infected individuals, there is a driving need to understand not only the biology of these viruses and how they remain undetected in host cells but also the mechanism(s) by which tumorigenesis occurs. One of the methods that has provided much insight into these processes is proteomics. Proteomics is the study of all the proteins that are encoded by a genome and allows for (i) identification of existing and novel proteins derived from a given genome, (ii) interrogation of protein-protein interactions within a system, and (iii) discovery of druggable targets for the treatment of malignancies. In this chapter, we explore how proteomics has contributed to our current understanding of gammaherpesvirus biology and their oncogenic processes, as well as the clinical applications of proteomics for the detection and treatment of gammaherpesvirus-associated cancers.
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Zhang Y, Ou M, Lin H, Lai L, Chen H, Chen J, Sui W, Xue W, Zhang R, Gan Q, Tang D, Sun X, Dong J, Yan Q, Dai Y. Proteomic analysis of differentially expressed proteins in the serum of patients with acute renal allograft rejection using iTRAQ labelling technology. Mol Med Rep 2020; 22:2329-2341. [PMID: 32705285 PMCID: PMC7411402 DOI: 10.3892/mmr.2020.11299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/07/2020] [Indexed: 12/24/2022] Open
Abstract
Transplantation is currently the best treatment for patients with end‑stage renal disease. However, acute rejection (AR) is the major source of failure in renal transplantation. The current best practice for the diagnosis of AR involves renal biopsy, but it is invasive, time‑consuming, costly and inconvenient. Sensitive and less invasive detection of AR episodes in renal transplant patients is essential to preserve allograft function. The present study applied isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry to analyze serum protein expression in patients with AR and healthy controls. Overall, 1,399 proteins were identified. Using a cut‑off of Q<0.05 and a fold change of >1.2 for the variation in expression, 109 proteins were identified to be differentially expressed between the AR and control groups, 72 of which were upregulated and 37 were downregulated. Several proteins, including properdin, keratin 1, lipoprotein(a) and vitamin D‑binding protein, may have roles in the pathogenesis of AR. The present study focused on iTRAQ‑based proteomic profiling of serum samples in AR. Insight from the present study may help advance the understanding of the molecular mechanisms of AR and identify potential novel biomarkers of AR for further characterization.
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Affiliation(s)
- Yue Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Hua Lin
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Liusheng Lai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Huaizhou Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Jiejing Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Weiguo Sui
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Ruohan Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Qing Gan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Xuyong Sun
- Department of Organ Transplantation, Institute of Transplant Medicine, No. 923 Hospital of People's Liberation Army, Guangxi Key Laboratory for Transplantation Medicine, Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi 530021, P.R. China
| | - Jianhui Dong
- Department of Organ Transplantation, Institute of Transplant Medicine, No. 923 Hospital of People's Liberation Army, Guangxi Key Laboratory for Transplantation Medicine, Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, Guangxi 530021, P.R. China
| | - Qiang Yan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
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Abstract
Introduction: Nasopharyngeal carcinoma (NPC) is a distinct head and neck squamous cell carcinoma in its etiological association of Epstein-Barr virus (EBV) infection, hidden anatomical location, remarkable racial and geographical distribution, and high incidence of locoregional recurrence or metastasis. Thanks to the advancements in proteomics in recent decades, more understanding of the disease etiology, carcinogenesis, and progression has been gained, potentially deciphering the molecular characteristics of the malignancy. Areas covered: In this review, we provide an overview of the proteomic aberrations that are likely involved or drive NPC development and progression, focusing on the contributions of major EBV-encoded factors, intercommunication with environment, protein features of high metastasis and therapy resistance, and protein-protein interactions that allow NPC cells to evade immune recognition and elimination. Finally, multistep carcinogenesis and subtypes of NPC from a proteomic perspective are inquired. Expert commentary: Proteomic studies have covered various aspects involved in NPC pathogenesis, yet much remains to be uncovered. Coherent study designs, optimal conditions for obtaining high-quality data, and compelling interpretation are critical in ensuring the emergence of good science out of NPC proteomics. NPC proteogenomics and proteoform analysis are two promising fields to promote the application of the proteomic findings from bench to bedside.
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Affiliation(s)
- Zhefeng Xiao
- a NHC Key Laboratory of Cancer Proteomics , Xiangya Hospital, Central South University , Changsha , P. R. China
| | - Zhuchu Chen
- a NHC Key Laboratory of Cancer Proteomics , Xiangya Hospital, Central South University , Changsha , P. R. China
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Shereck E, Day NS, Awasthi A, Ayello J, Chu Y, McGuinn C, van de Ven C, Lim MS, Cairo MS. Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56 Dim NK cells. Innate Immun 2019; 25:294-304. [PMID: 31068047 PMCID: PMC6830905 DOI: 10.1177/1753425919846584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unrelated cord blood (CB) is an excellent alternative as an allogeneic donor
source for stem cell transplantation. CB transplantation is associated with
lower incidence of severe acute graft versus host disease (GVHD) and chronic
GVHD but similar rates of malignant relapse compared with other unrelated donor
cell transplants. NK cells are critical innate immune components and the
comparison of CB vs. peripheral blood (PB) NK cells is relatively unknown. NK
cell receptor expression, cell function, and maturation may play a role in the
risk of relapse after CB transplant. We investigated CB vs. PB NK cell subset
cytotoxicity, function, receptor expression, and genomic and proteomic
signatures. The CB CD56dim compared with PB CD56dim
demonstrated significantly increased expression of NKG2A and NKG2D,
respectively. CB vs. PB CD56dim NK cells had significantly decreased
in vitro cytotoxicity against a variety of non-Hodgkin
lymphoma targets. Various proteins were significantly under- and over-expressed
in CB vs. PB CD56dim NK cells. Microarray analyses and qRT-PCR in CB
vs. PB CD56dim demonstrated significantly increased expression of
genes in cell regulation and development of apoptosis, respectively. In summary,
CB vs. PB CD56dim NK cells appear to be earlier in development, have
decreased functional activity, and increased capacity for programmed cell death,
suggesting that CB NK cells require functional and maturational stimulation to
achieve similar functional levels as PB CD56dim NK cells.
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Affiliation(s)
- Evan Shereck
- 1 Department of Pediatrics, Oregon Health and Science University, Portland, 97239, USA
| | - Nancy S Day
- 2 Department of Pediatrics, Columbia University, New York, USA
| | - Aradhana Awasthi
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | - Janet Ayello
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | - Yaya Chu
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA
| | | | | | - Megan S Lim
- 4 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Mitchell S Cairo
- 3 Department of Pediatrics, New York Medical College, Valhalla, USA.,5 Department of Medicine, New York Medical College, Valhalla, USA.,6 Department of Pathology, New York Medical College, Valhalla, USA.,7 Department of Microbiology and Immunology, New York Medical College, Valhalla, USA.,8 Department Cell Biology and Anatomy, New York Medical College, Valhalla, USA
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5
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WANG M, LIU G, LI H. Extraction of matrine from Sophora flavescens Ait. and evaluation of its inhibitory effects on human nasopharyngeal carcinoma CNE-2 cells. FOOD SCIENCE AND TECHNOLOGY 2018. [DOI: 10.1590/fst.24117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Xia L, Dai L, Zhu L, Hu W, Yang Q. Proteomic Analysis of IPEC-J2 Cells in Response to Coinfection by Porcine Transmissible Gastroenteritis Virus and Enterotoxigenic Escherichia coli K88. Proteomics Clin Appl 2018; 11. [PMID: 29090858 DOI: 10.1002/prca.201600137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 09/22/2017] [Indexed: 01/03/2023]
Abstract
SCOPE Piglet diarrhea causes large economic losses to the swine industry. Epidemiological investigations show that piglet diarrhea is often caused by mixed infections, but the mechanisms by which multiple microorganisms cause disease are unclear. EXPERIMENTAL DESIGN Because transmissible gastroenteritis virus (TGEV) and enterotoxigenic Escherichia coli K88 (ETEC K88) are important contributors to piglet diarrhea, coinfection experiments are conducted using porcine intestinal columnar epithelial cells (IPEC-J2) as a model system. In order to evaluate piglet diarrhea caused TGEV and ETEC K88, the authors examin the effects of coinfection in IPEC-J2 cells. In TGEV pre-infected IPEC-J2 cells, ETEC K88 adhesion is enhanced over uninfected cells. ETEC K88 is also found to inhibit the proliferation of TGEV. Additionally, cytokine levels (IL-1β, IL-6, IL-8, and TNF-α) in coinfected cells are lower than cells infected by TGEV alone, and higher than cells infected by ETEC K88 alone. LCMS/MS coupled to isobaric tags for relative and absolute quantification (iTRAQ) is used to profile expressed proteins in IPEC-J2 cells infected by TGEV alone, ETEC K88 alone, and by both agents together. RESULTS 77, 89, and 136 differentially expressed proteins are identified in TGEV infected, ETEC K88 infected, and coinfected cells, respectively. CONCLUSION AND CLINICAL RELEVANCE Based on these data, the authors suspect that integrin α5 might enable TGEV to promote ETEC K88 adhesion. This study is the first to analyze piglet diarrhea caused by TGEV-ETEC K88 coinfection using high-throughput quantitative proteomics. The results advance the understanding of coinfection and its role in causing piglet diarrhea.
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Affiliation(s)
- Lu Xia
- College of veterinary medicine, Nanjing Agricultural University, Jiangsu, PR China
| | - Lei Dai
- College of veterinary medicine, Nanjing Agricultural University, Jiangsu, PR China
| | - Liqi Zhu
- College of veterinary medicine, Nanjing Agricultural University, Jiangsu, PR China
| | - Weiwei Hu
- College of veterinary medicine, Nanjing Agricultural University, Jiangsu, PR China
| | - Qian Yang
- College of veterinary medicine, Nanjing Agricultural University, Jiangsu, PR China
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7
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Chen Z, Long L, Wang K, Cui F, Zhu L, Tao Y, Wu Q, Xiang M, Liang Y, Qiu S, Xiao Z, Yi B. Identification of nasopharyngeal carcinoma metastasis-related biomarkers by iTRAQ combined with 2D-LC-MS/MS. Oncotarget 2017; 7:34022-37. [PMID: 27145374 PMCID: PMC5085135 DOI: 10.18632/oncotarget.9067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/16/2016] [Indexed: 12/15/2022] Open
Abstract
To identify metastasis-related proteins in nasopharyngeal carcinoma (NPC), iTRAQ-tagging combined with 2D LC-MS/MS analysis was performed to identify the differentially expressed proteins (DEPs) in high metastatic NPC 5-8F cells and non-metastatic NPC 6-10B cells, and qRT-PCR and Western blotting were used to confirm DEPs. As a result, 101 DEPs were identified by proteomics, and 12 DEPs were selectively validated. We further detected expression of three DEPs (RAN, SQSTM1 and TRIM29) in a cohort of NPC tissue specimens to assess their value as NPC metastatic biomarkers, and found that combination of RAN, SQSTM1 and TRIM29 could discriminate metastatic NPC from non-metastatic NPC with a sensitivity of 88% and a specificity of 91%. TRIM29 and RAN expression level were closely correlated with lymph node and distant metastasis and clinical stage (P <0.05) in NPC patients. Finally, a combination of loss-of-function and gain-of-function approaches was performed to determine the effects of TRIM29 on NPC cell proliferation, migration, invasion and metastasis. The results showed that TRIM29 knockdown significantly attenuated while TRIM29 overexpression promoted NPC cell in vitro proliferation, migration and invasion and in vivo metastasis. The present data first time show that SQSTM1, RAN and TRIM29 are novel potential biomarkers for predicting NPC metastasis, demonstrate that TRIM29 is a metastasis-promoted protein of NPC.
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Affiliation(s)
- Zhen Chen
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lu Long
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Kun Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Facai Cui
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lepan Zhu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Ya Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Qiong Wu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Manlin Xiang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yunlai Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Shiyang Qiu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Zhiqiang Xiao
- The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Yi
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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Voltage-Dependent Anion Channel 1 Interacts with Ribonucleoprotein Complexes To Enhance Infectious Bursal Disease Virus Polymerase Activity. J Virol 2017; 91:JVI.00584-17. [PMID: 28592532 DOI: 10.1128/jvi.00584-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/28/2017] [Indexed: 02/05/2023] Open
Abstract
Infectious bursal disease virus (IBDV) is a double-stranded RNA (dsRNA) virus. Segment A contains two overlapping open reading frames (ORFs), which encode viral proteins VP2, VP3, VP4, and VP5. Segment B contains one ORF and encodes the viral RNA-dependent RNA polymerase, VP1. IBDV ribonucleoprotein complexes are composed of VP1, VP3, and dsRNA and play a critical role in mediating viral replication and transcription during the virus life cycle. In the present study, we identified a cellular factor, VDAC1, which was upregulated during IBDV infection and found to mediate IBDV polymerase activity. VDAC1 senses IBDV infection by interacting with viral proteins VP1 and VP3. This association is caused by RNA bridging, and all three proteins colocalize in the cytoplasm. Furthermore, small interfering RNA (siRNA)-mediated downregulation of VDAC1 resulted in a reduction in viral polymerase activity and a subsequent decrease in viral yield. Moreover, overexpression of VDAC1 enhanced IBDV polymerase activity. We also found that the viral protein VP3 can replace segment A to execute polymerase activity. A previous study showed that mutations in the C terminus of VP3 directly influence the formation of VP1-VP3 complexes. Our immunoprecipitation experiments demonstrated that protein-protein interactions between VDAC1 and VP3 and between VDAC1 and VP1 play a role in stabilizing the interaction between VP3 and VP1, further promoting IBDV polymerase activity.IMPORTANCE The cellular factor VDAC1 controls the entry and exit of mitochondrial metabolites and plays a pivotal role during intrinsic apoptosis by mediating the release of many apoptogenic molecules. Here we identify a novel role of VDAC1, showing that VDAC1 interacts with IBDV ribonucleoproteins (RNPs) and facilitates IBDV replication by enhancing IBDV polymerase activity through its ability to stabilize interactions in RNP complexes. To our knowledge, this is the first report that VDAC1 is specifically involved in regulating IBDV RNA polymerase activity, providing novel insight into virus-host interactions.
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Identification of CD14 as a potential biomarker of hepatocellular carcinoma using iTRAQ quantitative proteomics. Oncotarget 2017; 8:62011-62028. [PMID: 28977922 PMCID: PMC5617482 DOI: 10.18632/oncotarget.18782] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 05/14/2017] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors without effective diagnostic biomarkers. This study intended to dynamically analyze serum proteomics in different pathological stages of liver diseases, and discover potential diagnostic biomarkers for early HCC. Patients with hepatitis B virus (HBV) infection, liver cirrhosis (LC), or HCC together with healthy controls (HC) were enrolled. Proteins differentially expressed between groups were screened using isobaric tagging for relative and absolute quantitation (iTRAQ), and promising HCC biomarker candidates were subjected to bioinformatics analysis, including K-means clustering, gene ontology (GO) and string network analysis. Potential biomarkers were validated by Western blotting and enzyme-linked immunosorbent assay (ELISA), and their diagnostic performance was evaluated using receiver operating characteristic (ROC) curve analysis. Finally, 93 differentially expressed proteins were identified, of which 43 differed between HBV and HC, 70 between LC and HC, and 51 between HCC and HC. Expression levels of gelsolin (GELS) and sulfhydryl oxidase 1 (QSOX1) varied with disease state as follows: HC < HBV < LC < HCC. The reverse trend was observed with CD14. These iTRAQ results were confirmed by Western blotting and ELISA. Logistic regression and ROC curve analysis identified the optimal cut-off for alpha-fetoprotein (AFP), CD14 and AFP/CD14 was 191.4 ng/mL (AUC 0.646, 95%CI 0.467-0.825, sensitivity 31.6%, specificity 94.4%), 3.16 ng/mL (AUC 0.760, 95%CI 0.604-0.917, sensitivity 94.7%, specificity 50%) and 0.197 ng/mL (AUC 0.889, 95%CI 0.785-0.993, sensitivity 84.2%, specificity 83.3%) respectively. In conclusion, Assaying CD14 levels may complement AFP measurement for early detection of HCC.
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Lu M, Bai J, Xu B, Sun Q, Wei F, Tang X, Zhang H, Li J, Wang G, Yin Q, Li S. Effect of alpha-lipoic acid on relieving ammonia stress and hepatic proteomic analyses of broilers. Poult Sci 2017; 96:88-97. [DOI: 10.3382/ps/pew285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/21/2016] [Accepted: 07/01/2016] [Indexed: 11/20/2022] Open
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A Review: Proteomics in Nasopharyngeal Carcinoma. Int J Mol Sci 2015; 16:15497-530. [PMID: 26184160 PMCID: PMC4519910 DOI: 10.3390/ijms160715497] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 06/08/2015] [Accepted: 07/01/2015] [Indexed: 12/24/2022] Open
Abstract
Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies.
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Omics-based identification of biomarkers for nasopharyngeal carcinoma. DISEASE MARKERS 2015; 2015:762128. [PMID: 25999660 PMCID: PMC4427004 DOI: 10.1155/2015/762128] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/10/2015] [Indexed: 12/14/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a head and neck cancer that is highly found in distinct geographic areas, such as Southeast Asia. The management of NPC remains burdensome as the prognosis is poor due to the late presentation of the disease and the complex nature of NPC pathogenesis. Therefore, it is necessary to find effective molecular markers for early detection and therapeutic measure of NPC. In this paper, the discovery of molecular biomarker for NPC through the emerging omics technologies including genomics, miRNA-omics, transcriptomics, proteomics, and metabolomics will be extensively reviewed. These markers have been shown to play roles in various cellular pathways in NPC progression. The knowledge on their function will help us understand in more detail the complexity in tumor biology, leading to the better strategies for early detection, outcome prediction, detection of disease recurrence, and therapeutic approach.
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An K, Fang L, Luo R, Wang D, Xie L, Yang J, Chen H, Xiao S. Quantitative proteomic analysis reveals that transmissible gastroenteritis virus activates the JAK-STAT1 signaling pathway. J Proteome Res 2014; 13:5376-90. [PMID: 25357264 DOI: 10.1021/pr500173p] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transmissible gastroenteritis virus (TGEV), a porcine enteropathogenic coronavirus, causes lethal watery diarrhea and severe dehydration in piglets. In this study, liquid chromatography-tandem mass spectrometry coupled to isobaric tags for relative and absolute quantification labeling was used to quantitatively identify differentially expressed cellular proteins after TGEV infection in PK-15 cells. In total, 162 differentially expressed cellular proteins were identified, including 60 upregulated proteins and 102 downregulated proteins. These differentially expressed proteins were involved in the cell cycle, cellular growth and proliferation, the innate immune response, etc. Interestingly, many upregulated proteins were associated with interferon signaling, especially signal transducer and activator of transcription 1 (STAT1) and interferon-stimulated genes (ISGs). Immunoblotting and real-time quantitative reverse transcription polymerase chain reaction demonstrated that TGEV infection induces STAT1 phosphorylation and nuclear translocation, as well as ISG expression. This study for the first time reveals that TGEV induces interferon signaling from the point of proteomic analysis.
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Affiliation(s)
- Kang An
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, Hubei China
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14
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El-Mallawany NK, Day N, Ayello J, Van de Ven C, Conlon K, Fermin D, Basrur V, Elenitoba-Johnson K, Lim M, Cairo MS. Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma. Eur J Cancer 2014; 51:92-100. [PMID: 25466511 DOI: 10.1016/j.ejca.2014.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/07/2014] [Accepted: 10/20/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Burkitt lymphoma (BL) is the most common non-Hodgkin lymphoma in children worldwide and the most common paediatric malignancy in sub-Saharan Africa. The endemic (eBL) and sporadic (sBL) variants have distinct epidemiologic and virologic characteristics. Although gene expression studies have defined the transcriptional profiles of both, their proteomic signatures have not been studied. METHODS We compared the proteomic expression profiles using differential mass spectrometry-based isotope tag for relative and absolute quantitation (iTRAQ) analysis of a cell line representing Epstein-Barr virus (EBV)+ eBL, EBV+ and EBV- sBL, and EBV+/- normal B cells from healthy donors. RESULTS In total, there were 144 differentially expressed proteins with a statistically significant false discovery rate (FDR) of ⩽0.2. Results revealed over-expression of specific proteins with well-established links to lymphomagenesis such as TUBB2C (FDR 0.05), UCHL1 (FDR 0.05) and HSP90AB1 (FDR 0.1). Distinct characteristics based upon the epidemiologic and virologic subtypes of BL were also identified. In sBL, PCNA (FDR 0.05) and SLC3A2 (FDR 0.1) were significantly over-expressed. In eBL, C1QBP (FDR 0.1) and ENO1 (FDR 0.25) were significantly over-expressed. Comparison of EBV+ to EBV- BL cell lines and B cells revealed significant over-expression of DDX3X (FDR 0.1). Proteins were validated using Western blot analysis. CONCLUSION Our results suggest unique signal transduction pathways associated with EBV infection and epidemiological subtype of BL that may contribute to lymphomagenesis. These proteomic findings provide potential diagnostic, prognostic and therapeutic links to BL.
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Affiliation(s)
| | - Nancy Day
- Department of Pediatrics, Columbia University, New York, NY, United States
| | - Janet Ayello
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Carmella Van de Ven
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Kevin Conlon
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | | | - Megan Lim
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Mitchell S Cairo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States; Department of Medicine, New York Medical College, Valhalla, NY, United States; Department of Pathology, New York Medical College, Valhalla, NY, United States; Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, United States; Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States.
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OWEN CHRISTOPHERB, HUGHES DAVIDJ, BAQUERO-PEREZ BELINDA, BERNDT ANJA, SCHUMANN SOPHIE, JACKSON BRIANR, WHITEHOUSE ADRIAN. Utilising proteomic approaches to understand oncogenic human herpesviruses (Review). Mol Clin Oncol 2014; 2:891-903. [PMID: 25279171 PMCID: PMC4179824 DOI: 10.3892/mco.2014.341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/10/2014] [Indexed: 12/16/2022] Open
Abstract
The γ-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are successful pathogens, each infecting a large proportion of the human population. These viruses persist for the life of the host and may each contribute to a number of malignancies, for which there are currently no cures. Large-scale proteomic-based approaches provide an excellent means of increasing the collective understanding of the proteomes of these complex viruses and elucidating their numerous interactions within the infected host cell. These large-scale studies are important for the identification of the intricacies of viral infection and the development of novel therapeutics against these two important pathogens.
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Affiliation(s)
- CHRISTOPHER B. OWEN
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - DAVID J. HUGHES
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - BELINDA BAQUERO-PEREZ
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - ANJA BERNDT
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - SOPHIE SCHUMANN
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - BRIAN R. JACKSON
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - ADRIAN WHITEHOUSE
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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16
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Dihydromyricetin ameliorates the oxidative stress response induced by methylglyoxal via the AMPK/GLUT4 signaling pathway in PC12 cells. Brain Res Bull 2014; 109:117-26. [PMID: 25451453 DOI: 10.1016/j.brainresbull.2014.10.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/03/2014] [Accepted: 10/20/2014] [Indexed: 01/01/2023]
Abstract
Dihydromyricetin (DMY), the major bioactive flavonoid ingredient extracted from the leaves of Ampelopsis grossedentata (Hand.-Mazz) W.T. Wang, displays multiple pharmacological activities, including oxidation resistance, antitumor properties and free radical scavenging capacities. However, the role of DMY in methylglyoxal (MG)-induced diabetes-associated cognitive decline and its underlying molecular mechanisms are unclear. The aim of the present study was to evaluate the effects of DMY on oxidative stress and glucose transport activity in a MG-induced PC12 cell line and to explore the related mechanisms. The effects of DMY on cell survival and apoptosis were examined, and the dysregulation of intracellular Ca(2+) was determined. Oxidative stress was evaluated by monitoring ROS production and the glutathione to glutathione disulfide ratio. The effects of DMY on glucose metabolism were investigated using a fluorescently labeled deoxyglucose analog and by measuring ATP and lactate production. Western blot analysis was performed to examine the protein levels of glyoxalase I (Glo-1), glucose transporter 4 (GLUT4), AMP-activated protein kinase (AMPKα) and phosphorylated AMPKα (p-AMPKα). The results revealed that DMY suppressed cellular oxidative stress in PC12 cells and balanced glucose metabolism. Additionally, DMY reduced GLUT4 translocation dysfunction and increased Glo-1 and p-AMPKα expression. We found that DMY protected PC12 cells against MG-induced apoptosis and glycometabolic disorders, at least in part by restraining the hyperactivation of p-AMPK activity and normalizing the translocation of GLUT4 from the intracellular compartment, resulting in a balance in glucose uptake. This result indicates that DMY may serve as a novel and effective candidate agent to treat diabetic encephalopathy by reducing the toxicity of MG.
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17
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Ma R, Zhang Y, Liu H, Ning P. Proteome profile of swine testicular cells infected with porcine transmissible gastroenteritis coronavirus. PLoS One 2014; 9:e110647. [PMID: 25333634 PMCID: PMC4204940 DOI: 10.1371/journal.pone.0110647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/19/2014] [Indexed: 02/06/2023] Open
Abstract
The interactions occurring between a virus and a host cell during a viral infection are complex. The purpose of this paper was to analyze altered cellular protein levels in porcine transmissible gastroenteritis coronavirus (TGEV)-infected swine testicular (ST) cells in order to determine potential virus-host interactions. A proteomic approach using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled two-dimensional liquid chromatography-tandem mass spectrometry identification was conducted on the TGEV-infected ST cells. The results showed that the 4-plex iTRAQ-based quantitative approach identified 4,112 proteins, 146 of which showed significant changes in expression 48 h after infection. At 64 h post infection, 219 of these proteins showed significant change, further indicating that a larger number of proteomic changes appear to occur during the later stages of infection. Gene ontology analysis of the altered proteins showed enrichment in multiple biological processes, including cell adhesion, response to stress, generation of precursor metabolites and energy, cell motility, protein complex assembly, growth, developmental maturation, immune system process, extracellular matrix organization, locomotion, cell-cell signaling, neurological system process, and cell junction organization. Changes in the expression levels of transforming growth factor beta 1 (TGF-β1), caspase-8, and heat shock protein 90 alpha (HSP90α) were also verified by western blot analysis. To our knowledge, this study is the first time the response profile of ST host cells following TGEV infection has been analyzed using iTRAQ technology, and our description of the late proteomic changes that are occurring after the time of vigorous viral production are novel. Therefore, this study provides a solid foundation for further investigation, and will likely help us to better understand the mechanisms of TGEV infection and pathogenesis.
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MESH Headings
- Animals
- Cell Line
- Chromatography, Liquid
- Gastroenteritis, Transmissible, of Swine/genetics
- Gastroenteritis, Transmissible, of Swine/metabolism
- Gastroenteritis, Transmissible, of Swine/pathology
- Gastroenteritis, Transmissible, of Swine/virology
- Gene Expression Regulation, Viral
- Male
- Proteome/genetics
- Swine
- Testis/metabolism
- Testis/pathology
- Testis/virology
- Transmissible gastroenteritis virus/genetics
- Transmissible gastroenteritis virus/pathogenicity
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Affiliation(s)
- Ruili Ma
- College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- * E-mail:
| | - Haiquan Liu
- School of Computer Science and Engineering, Xi’an Technological University, Xi’an, Shaanxi, China
| | - Pengbo Ning
- College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
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18
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Liu J, Bai J, Zhang L, Hou C, Li Y, Jiang P. Proteomic alteration of PK-15 cells after infection by porcine circovirus type 2. Virus Genes 2014; 49:400-16. [PMID: 25103791 PMCID: PMC7089180 DOI: 10.1007/s11262-014-1106-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/28/2014] [Indexed: 12/11/2022]
Abstract
Porcine circovirus type 2 (PCV2) has been identified as the essential causal agent of post-weaning multisystemic wasting syndrome, which has spread worldwide. To discover cellular protein responses of PK-15 cells to PCV2 infection, two-dimensional liquid chromatography-tandem mass spectrometry (MS) coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling was employed to quantitatively identify the proteins that were differentially expressed in PK-15 from the PCV2-infected group compared to the uninfected control group. A total of 196 cellular proteins in PK-15 that were significantly altered at different time periods post-infection were identified. These differentially expressed proteins were related to the biological processes of binding, cell structure, signal transduction, cell adhesion, etc. and their interactions. Moreover, some of these proteins were further confirmed by Western blot. The high number of differentially expressed proteins identified should be very useful in elucidating the mechanism of replication and pathogenesis of PCV2 in the future.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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19
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Xiao L, Xiao T, Wang ZM, Cho WCS, Xiao ZQ. Biomarker discovery of nasopharyngeal carcinoma by proteomics. Expert Rev Proteomics 2014; 11:215-25. [PMID: 24611579 DOI: 10.1586/14789450.2014.897613] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in southern China and southern Asia, and poses one of the most serious public health problems in these areas. Early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC remain a challenge. Discovery of diagnostic and predictive biomarkers is an ideal way to achieve these objectives. Proteomics has great potential in identifying cancer biomarkers. Comparative proteomics has identified a large number of potential biomarkers associated with NPC, although the clinical performance of such biomarkers needs to be further validated. In this article, we review the latest discovery and progress of biomarkers for early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC, inform the readers of the current status of proteomics-based NPC biomarker findings and suggest avenues for future work.
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Affiliation(s)
- Liang Xiao
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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20
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Papachristou EK, Roumeliotis TI, Chrysagi A, Trigoni C, Charvalos E, Townsend PA, Pavlakis K, Garbis SD. The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: the detection of the human papillomavirus at the protein level. J Proteome Res 2013; 12:2078-89. [PMID: 23510160 DOI: 10.1021/pr301067r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ThinPrep cervical smear is widely used in clinical practice for the cytological and molecular screening against abnormal cells and Human Papillomavirus (HPV) infection. Current advancements made to LC-MS proteomics include the use of stable isotope labeling for the in-depth analysis of proteins in complex clinical specimens. Such approaches have yet to be realized for ThinPrep clinical specimens. In this study, an LC-MS method based on isobaric (iTRAQ) labeling and high-resolution FT-Orbitrap mass spectrometry was used for the proteomic analysis of 23 human ThinPrep smear specimens. Tandem mass spectrometry analysis was performed with both nitrogen high collision dissociation (HCD MS/MS) and helium collision induced dissociation (CID MS/MS) peptide fragmentation modes. The analysis of three 8-plex sample sets yielded the identification of over 3200 unique proteins at FDR < 1%, of which over 2300 proteins were quantitatively profiled in at least one of the three experiments. The interindividual variability served to define the required sample size needed to identify significant protein expression differences. The degree of in-depth proteome coverage allowed the detection of 6 HPV-derived proteins including the high-risk HPV16 type in the specimens tested. The presence of the HPV strains of origin was also confirmed with PCR-hybridization molecular methods. This proof-of-principle study constitutes the first ever report on the nontargeted analysis of HPV proteins in human ThinPrep clinical specimens with high-resolution mass spectrometry. A further testament to the sensitivity and selectivity of the proposed study method was the confident detection of a significant number of phosphopeptides in these specimens.
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Affiliation(s)
- Evaggelia K Papachristou
- Institute for Life Sciences, Centre for Proteomic Research, University of Southampton, Highfield Campus, Southampton, UK
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21
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EBV up-regulates cytochrome c through VDAC1 regulations and decreases the release of cytoplasmic Ca2+ in the NPC cell line. Cell Biol Int 2012; 36:733-8. [PMID: 22497278 DOI: 10.1042/cbi20110368] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
EBV (Epstein-Barr virus) is considered to be a major factor that causes NPC (nasopharyngeal carcinoma), which is one of the sneakiest cancers frequently occurring in Southeast Asia and Southern China. Apoptosis and pro-apoptotic signals have been studied for decades; however, few have extended the prevailing view of EBV to its impact on NPC in perspective of apoptosis. One of the important proteins named VDAC1 (voltage-dependent anion protein 1) on the mitochondrial outer membrane controls the pro-apoptotic signals in mammalian cells. The impact of EBV infection on VDAC1 and related apoptotic signals remains unclear. In order to study the VDAC1's role in EBV-infected NPC cells, we employ siRNA (small interfering RNA) inhibition to analyse the release of Ca2+ and Cyto c (cytochrome c) signals in the cytoplasm, as they are important pro-apoptotic signals. The results show a decrease of Ca2+ release and up-regulation of Cyto c with EBV infection. After siRNA transfection, the dysregulation of Cyto c is neutralized, which is evidence that the level of Cyto c release in virus-infected NPC cells is the as same as that of non-infected NPC cells. This result indicates that EBV infection changes the cytoplasmic level of Cyto c through regulating VDAC1. In summary, this study reports that EBV changes the release of Ca2+ and Cyto c in the cytoplasm of NPC cells, and that Cyto c changes are mediated by VDAC1 regulation.
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22
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Affiliation(s)
| | - Sinéad M. Miggin
- Immune Signalling Group; Institute of Immunology; Department of Biology; National University of Ireland Maynooth; Co. Kildare Ireland
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23
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Translational research in infectious disease: current paradigms and challenges ahead. Transl Res 2012; 159:430-53. [PMID: 22633095 PMCID: PMC3361696 DOI: 10.1016/j.trsl.2011.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/23/2011] [Accepted: 12/24/2012] [Indexed: 12/25/2022]
Abstract
In recent years, the biomedical community has witnessed a rapid scientific and technologic evolution after the development and refinement of high-throughput methodologies. Concurrently and consequentially, the scientific perspective has changed from the reductionist approach of meticulously analyzing the fine details of a single component of biology to the "holistic" approach of broadmindedly examining the globally interacting elements of biological systems. The emergence of this new way of thinking has brought about a scientific revolution in which genomics, proteomics, metabolomics, and other "omics" have become the predominant tools by which large amounts of data are amassed, analyzed, and applied to complex questions of biology that were previously unsolvable. This enormous transformation of basic science research and the ensuing plethora of promising data, especially in the realm of human health and disease, have unfortunately not been followed by a parallel increase in the clinical application of this information. On the contrary, the number of new potential drugs in development has been decreasing steadily, suggesting the existence of roadblocks that prevent the translation of promising research into medically relevant therapeutic or diagnostic application. In this article, we will review, in a noninclusive fashion, several recent scientific advancements in the field of translational research, with a specific focus on how they relate to infectious disease. We will also present a current picture of the limitations and challenges that exist for translational research, as well as ways that have been proposed by the National Institutes of Health to improve the state of this field.
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Key Words
- 2-de, 2-dimensional electrophoresis
- 2-d dige, 2-dimensional differential in-gel electrophoresis
- cf, cystic fibrosis
- ctsa, clinical and translational science awards program
- ebv, epstein-barr virus
- fda, u.s. food and drug administration
- gwas, genome-wide association studies
- hcv, hepatitis c virus
- hmp, human microbiome project
- hplc, high-pressure liquid chromatography
- lc, liquid chromatography
- lsb, laboratory of systems biology
- mab, monoclonal antibody
- mrm/srm, multiple reaction monitoring/selective reaction monitoring
- ms, mass spectrometry
- ms/ms, tandem mass spectrometry
- ncats, national center for advancing translational sciences
- ncrr, national center of research resources
- niaid, national institute of allergy and infectious disease
- nih, national institutes of health
- nme, new molecular entity
- nmr, nuclear magnetic resonance
- pbmc, peripheral blood mononuclear cell
- pcr, polymerase chain reaction
- prr, pathogen recognition receptor
- qqq, triple quadrupole mass spectrometry
- sars-cov, coronavirus associated with severe acute respiratory syndrome
- snp, single nucleotide polymorphism
- tb, tuberculosis
- uti, urinary tract infection
- yfv, yellow fever virus
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24
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Lu Q, Bai J, Zhang L, Liu J, Jiang Z, Michal JJ, He Q, Jiang P. Two-Dimensional Liquid Chromatography–Tandem Mass Spectrometry Coupled with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) Labeling Approach Revealed First Proteome Profiles of Pulmonary Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus. J Proteome Res 2012; 11:2890-903. [DOI: 10.1021/pr201266z] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Qi Lu
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Bai
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Lili Zhang
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Liu
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351,
United States
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351,
United States
| | - Qindong He
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Jiang
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
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25
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Misra RV, Ahmod NZ, Parker R, Fang M, Shah H, Gharbia S. Developing an integrated proteo-genomic approach for the characterisation of biomarkers for the identification of Bacillus anthracis. J Microbiol Methods 2011; 88:237-47. [PMID: 22178189 DOI: 10.1016/j.mimet.2011.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis is the causative agent of anthrax, an acute and often fatal disease in humans. Due to the high genomic relatedness within the Bacillus cereus group of species it is a challenge to identify B. anthracis consistently. Alternative strategies such as proteomics coupled with mass spectrometry (MS) provide a powerful approach for biomarker discovery. However, validating and evaluating these markers, particularly for genetically homogeneous species such as B. anthracis are challenging. The objective of this study is to develop a robust biomarker discovery and validation pipeline, using proteomic methodology combined with in silico and molecular approaches, to determine a biomarker list, using B. anthracis as a model. In this exploratory study we profiled the proteome of B. anthracis and genetically related species using GeLC-Liquid Chromatography MS/MS (GeLC-LC MS/MS), identifying peptides that could be used to detect B. anthracis. Peptides were filtered to remove low quality identifications. Using comparative bioinformatic approaches, matching and searching against genomic sequence data a shortlist of peptide biomarkers was determined and validated using DNA sequencing, against a panel of closely related strains, to determine marker specificity. Further validation was performed using MS quantitation methods to assess sensitivity and specificity. A biomarker discovery pipeline was successfully developed in this study, comprising four distinct stages: proteome profiling, comparative bioinformatic validation, DNA sequencing and MS validation. Using the pipeline, 5379 peptides specific for Bacillus species and 36 peptides specific for B. anthracis were identified and validated. The 36 peptides, representing 30 proteins were derived from over 15 different clusters of orthologous group categories, including proteins involved in transcription, energy production/conservation as well as multifunctional proteins. We demonstrated that the peptide biomarkers identified in this study could be detected in a complex background, in which 0.1 μg of protein extract from B. anthracis was spiked into 9.90 μg of B. cereus protein extracts. The integration of both stable non-redundant peptides with molecular methodology for marker discovery and validation, improves the robustness of identifying and characterising candidate biomarkers for the identification of bacteria such as B. anthracis.
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Affiliation(s)
- Raju V Misra
- Department for Bioanalysis and Horizon Technologies, Health Protection Agency, 61 Colindale Avenue, London NW95EQ, United Kingdom.
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26
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Zhou Y, Chen WN. iTRAQ-coupled 2-D LC–MS/MS analysis of cytoplasmic protein profile in Escherichia coli incubated with apidaecin IB. J Proteomics 2011; 75:511-6. [DOI: 10.1016/j.jprot.2011.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/11/2011] [Accepted: 08/18/2011] [Indexed: 11/27/2022]
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27
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Sui W, Tang D, Zou G, Chen J, Ou M, Zhang Y, Dai Y. Differential proteomic analysis of renal tissue in lupus nephritis using iTRAQ reagent technology. Rheumatol Int 2011; 32:3537-43. [DOI: 10.1007/s00296-011-2207-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 10/22/2011] [Indexed: 10/15/2022]
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