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Qin S, Gao K, Tian Z. Comprehensive characterization of differential glycation in hepatocellular carcinoma using tissue proteomics with stable isotopic labeling. Anal Bioanal Chem 2024:10.1007/s00216-024-05392-9. [PMID: 38922433 DOI: 10.1007/s00216-024-05392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/17/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
Glycation is a non-enzymatic posttranslational modification coming from the reaction between reducing sugars and free amino groups in proteins, where early glycation products (fructosyl-lysine, FL) and advanced glycation end products (AGEs) are formed. The occurrence of glycation and accumulation of AGEs have been closely associated with hepatocellular carcinoma (HCC). Here, we reported the characterization of differential glycation in HCC using tissue proteomics with stable isotopic labeling; early glycation-modified peptides were enriched with boronate affinity chromatography (BAC), and AGEs-modified peptides were fractionated with basic reversed-phase separation. By this integrated approach, 3717 and 1137 early and advanced glycated peptides corresponding to 4007 sites on 1484 proteins were identified with a false discovery rate (FDR) of no more than 1%. One hundred fifty-five sites were modified with both early and advanced end glycation products. Five early and 7 advanced glycated peptides were quantified to be differentially expressed in HCC tissues relative to paired adjacent tissues. Most (8 out of 10) of the proteins corresponding to the differential glycated peptides have previously been reported with dysregulation in HCC. The results together may deepen our knowledge of glycation as well as provide insights for therapeutics.
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Affiliation(s)
- Shanshan Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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2
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Chai B, Li Y, Guo Y, Zhang Z, Jia K, Chai X, Suo Y. ETV7 promotes colorectal cancer progression through upregulation of IFIT3. Funct Integr Genomics 2024; 24:8. [PMID: 38200280 PMCID: PMC10781848 DOI: 10.1007/s10142-023-01282-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/04/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024]
Abstract
Members of the E26 transformation-specific (ETS) variant transcription factor family act as either tumor suppressors or oncogenic factors in numerous types of cancer. ETS variant transcription factor 7 (ETV7) participates in the development of malignant tumors, whereas its involvement in colorectal cancer (CRC) is less clear. In this study, The Cancer Genome Atlas (TCGA) and immunochemistry staining were applied to check the clinical relevance of ETV7 and interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) in CRC patients. Overexpression and knockdown of ETV7 and IFIT3 were conducted by transfecting the cells with pCDNA3.1 plasmids and siRNAs, respectively. Western blotting was used to detect the protein expression of ETV7 in CRC cells. Cell Counting Kit-8, cell colony formation, and Transwell assays, as well as flow cytometry, were used to evaluate the proliferation, migration, cell cycle, and apoptosis of CRC cells. Furthermore, western blotting, RT-qPCR, and luciferase assay were used to explore the regulation of ETV7 on IFIT3. Rescue assay was used to investigate the significance of ETV7/IFIT3 axis on CRC progression. We found that ETV7 was upregulated in CRC tissues and cells. Overexpression of ETV7 stimulated the proliferation, migration, and cell cycle amplification, and reduced the apoptosis of CRC cells. Downregulation of ETV7 exerted the opposite effect on CRC cell progression. Moreover, we demonstrated that ETV7 stimulated the transcription activity, the mRNA and protein expression of IFIT3 in CRC cells. There was a positive correlation between ETV7 and IFIT3 in CRC patients. IFIT3 knockdown reversed the promotive effect exerted by overexpression of ETV7 on the amplification and migration of CRC cells. By contrast, overexpression of IFIT3 blocked the inhibitory effect of ETV7-targeting siRNA. In summary, ETV7 induces progression of CRC by activating the transcriptional expression of IFIT3. The EVT7/IFIT3 axis may be a novel target for CRC therapy.
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Affiliation(s)
- Bao Chai
- Department of Gastroenterology, Shanxi Academy of Medical Science, Shanxi Bethune Hospital, Taiyuan, China
| | - Yanjun Li
- Department of Surgery, Shanxi Academy of Medical Science, Shanxi Bethune Hospital, Taiyuan, China
| | - Yarong Guo
- Department of Oncology, The First Affiliated Hospital of Shanxi Medical University, 85 South Jiefang Road, TaiyuanTaiyuan, 030001, Shanxi Province, China.
| | - Zhuowei Zhang
- Medical Imaging Department, Shanxi Medical University, Taiyuan, China
| | - Kai Jia
- Department of Surgery, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinhao Chai
- Department of Oncology, The First Affiliated Hospital of Shanxi Medical University, 85 South Jiefang Road, TaiyuanTaiyuan, 030001, Shanxi Province, China
| | - Yuhong Suo
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Taiyuan, China
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Meškytė EM, Pezzè L, Bartolomei L, Forcato M, Bocci IA, Bertalot G, Barbareschi M, Oliveira-Ferrer L, Bisio A, Bicciato S, Baltriukienė D, Ciribilli Y. ETV7 reduces inflammatory responses in breast cancer cells by repressing the TNFR1/NF-κB axis. Cell Death Dis 2023; 14:263. [PMID: 37041130 PMCID: PMC10089821 DOI: 10.1038/s41419-023-05718-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 04/13/2023]
Abstract
The transcription factor ETV7 is an oncoprotein that is up-regulated in all breast cancer (BC) types. We have recently demonstrated that ETV7 promoted breast cancer progression by increasing cancer cell proliferation and stemness and was also involved in the development of chemo- and radio-resistance. However, the roles of ETV7 in breast cancer inflammation have yet to be studied. Gene ontology analysis previously performed on BC cells stably over-expressing ETV7 demonstrated that ETV7 was involved in the suppression of innate immune and inflammatory responses. To better decipher the involvement of ETV7 in these signaling pathways, in this study, we identified TNFRSF1A, encoding for the main receptor of TNF-α, TNFR1, as one of the genes down-regulated by ETV7. We demonstrated that ETV7 directly binds to the intron I of this gene, and we showed that the ETV7-mediated down-regulation of TNFRSF1A reduced the activation of NF-κB signaling. Furthermore, in this study, we unveiled a potential crosstalk between ETV7 and STAT3, another master regulator of inflammation. While it is known that STAT3 directly up-regulates the expression of TNFRSF1A, here we demonstrated that ETV7 reduces the ability of STAT3 to bind to the TNFRSF1A gene via a competitive mechanism, recruiting repressive chromatin remodelers, which results in the repression of its transcription. The inverse correlation between ETV7 and TNFRSF1A was confirmed also in different cohorts of BC patients. These results suggest that ETV7 can reduce the inflammatory responses in breast cancer through the down-regulation of TNFRSF1A.
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Affiliation(s)
- Erna Marija Meškytė
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Laura Pezzè
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Alia Therapeutics, s.r.l., Trento, Italy
| | - Laura Bartolomei
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Irene Adelaide Bocci
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institut für Zellbiologie, Universitätsklinikum Essen, Essen, Germany
| | - Giovanni Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | - Mattia Barbareschi
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | | | - Alessandra Bisio
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daiva Baltriukienė
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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Lambrecht C, Ferreira GB, Omella JD, Libbrecht L, DE Vos R, Derua R, Mathieu C, Overbergh L, Waelkens E, Janssens V. Differential Proteomic Analysis of Hepatocellular Carcinomas from Ppp2r5d Knockout Mice and Normal (Knockout) Livers. Cancer Genomics Proteomics 2021; 17:669-685. [PMID: 33099469 DOI: 10.21873/cgp.20222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the major type of primary liver cancer. Mice lacking the tumor-suppressive protein phosphatase 2A subunit B56δ (Ppp2r5d) spontaneously develop HCC, correlating with increased c-MYC oncogenicity. MATERIALS AND METHODS We used two-dimensional difference gel electrophoresis-coupled matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to identify differential proteomes of livers from wild-type, non-cancerous and HCC-affected B56δ knockout mice. RESULTS A total of 23 proteins were differentially expressed/regulated in liver between wild-type and non-cancerous knockout mice, and 119 between non-cancerous and HCC knockout mice ('cancer proteins'). Overlap with our reported differential transcriptome data was poor. Overall, 56% of cancer proteins were reported before in HCC proteomics studies; 44% were novel. Gene Ontology analysis revealed cancer proteins mainly associated with liver metabolism (18%) and mitochondria (15%). Ingenuity Pathway Analysis identified 'cancer' and 'gastrointestinal disease' as top hits. CONCLUSION We identified several proteins for further exploration as novel potential HCC biomarkers, and independently underscored the relevance of Ppp2r5d knockout mice as a valuable hepatocarcinogenesis model.
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Affiliation(s)
- Caroline Lambrecht
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Gabriela Bomfim Ferreira
- Clinical and Experimental Endocrinology, Department Clinical and Experimental Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Judit DomÈnech Omella
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Louis Libbrecht
- Department of Pathology, Université Catholique de Louvain (UCL), Brussels, Belgium
| | - Rita DE Vos
- Translational Cell and Tissue Research, Department Imaging and Pathology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Chantal Mathieu
- Clinical and Experimental Endocrinology, Department Clinical and Experimental Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Lut Overbergh
- Clinical and Experimental Endocrinology, Department Clinical and Experimental Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Etienne Waelkens
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium .,LKI, KU Leuven Cancer Institute, Leuven, Belgium
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5
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Sun R, Xu Y, Zhang H, Yang Q, Wang K, Shi Y, Wang Z. Mechanistic Modeling of Gene Regulation and Metabolism Identifies Potential Targets for Hepatocellular Carcinoma. Front Genet 2020; 11:595242. [PMID: 33424926 PMCID: PMC7786279 DOI: 10.3389/fgene.2020.595242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the predominant form of liver cancer and has long been among the top three cancers that cause the most deaths worldwide. Therapeutic options for HCC are limited due to the pronounced tumor heterogeneity. Thus, there is a critical need to study HCC from a systems point of view to discover effective therapeutic targets, such as through the systematic study of disease perturbation in both regulation and metabolism using a unified model. Such integration makes sense for cancers as it links one of the dominant physiological features of cancers (growth, which is driven by metabolic networks) with the primary available omics data source, transcriptomics (which is systematically integrated with metabolism through the regulatory-metabolic network model). Here, we developed an integrated transcriptional regulatory-metabolic model for HCC molecular stratification and the prediction of potential therapeutic targets. To predict transcription factors (TFs) and target genes affecting tumorigenesis, we used two algorithms to reconstruct the genome-scale transcriptional regulatory networks for HCC and normal liver tissue. which were then integrated with corresponding constraint-based metabolic models. Five key TFs affecting cancer cell growth were identified. They included the regulator CREB3L3, which has been associated with poor prognosis. Comprehensive personalized metabolic analysis based on models generated from data of liver HCC in The Cancer Genome Atlas revealed 18 genes essential for tumorigenesis in all three subtypes of patients stratified based on the non-negative matrix factorization method and two other genes (ACADSB and CMPK1) that have been strongly correlated with lower overall survival subtype. Among these 20 genes, 11 are targeted by approved drugs for cancers or cancer-related diseases, and six other genes have corresponding drugs being evaluated experimentally or investigationally. The remaining three genes represent potential targets. We also validated the stratification and prognosis results by an independent dataset of HCC cohort samples (LIRI-JP) from the International Cancer Genome Consortium database. In addition, microRNAs targeting key TFs and genes were also involved in established cancer-related pathways. Taken together, the multi-scale regulatory-metabolic model provided a new approach to assess key mechanisms of HCC cell proliferation in the context of systems and suggested potential targets.
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Affiliation(s)
| | | | | | | | | | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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6
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Multiplexed Proteomic Approach for Identification of Serum Biomarkers in Hepatocellular Carcinoma Patients with Normal AFP. J Clin Med 2020; 9:jcm9020323. [PMID: 31979338 PMCID: PMC7074125 DOI: 10.3390/jcm9020323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023] Open
Abstract
Alpha fetoprotein (AFP) has been used as a serologic indicator of hepatocellular carcinoma (HCC). We aimed to identify an HCC-specific serum biomarker for diagnosis using a multiplexed proteomic technique in HCC patients with normal AFP levels. A total of 152 patients were included from Guro Hospital, Korea University. Among 267 identified proteins, 28 and 86 proteins showed at least a two-fold elevation or reduction in expression, respectively. Multiple reaction monitoring (MRM) analysis of 41 proteins revealed 10 proteins were differentially expressed in patients with liver cirrhosis and HCC patients with normal AFP. A combination of tripartite motif22 (Trim22), seprase, and bone morphogenetic protein1 had an area under receiver operating characteristic of 0.957 for HCC diagnosis. Real-time PCR and western blot analysis of the paired tumor/non-tumor liver tissue in HCC revealed a reduced expression of Trim22 in the tumor tissue. Also, serum levels of Trim22 were significantly reduced in HCC patients with normal AFP compared to those with liver cirrhosis (p = 0.032). Inhibition of Trim22 increased cellular proliferation in human hepatoma cell lines, whereas overexpression of Trim22 decreased cellular proliferation in hepatoma cell lines. In conclusion, the combination of three serum markers improved the chance of diagnosing HCC. MRM-based quantification of the serum protein in patients with normal AFP provides the potential for early diagnosis of HCC.
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7
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Schlichtemeier SM, Nahm CB, Xue A, Gill AJ, Smith RC, Hugh TJ. SELDI-TOF MS Analysis of Hepatocellular Carcinoma in an Australian Cohort. J Surg Res 2019; 238:127-136. [PMID: 30771682 DOI: 10.1016/j.jss.2019.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 11/05/2018] [Accepted: 01/04/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cause of cancer death worldwide. Resection offers the best chance of long-term survival, but a consistent adverse prognostic factor is the presence of microvascular invasion (MVI). In this study, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), a high throughput method of analyzing complex samples, was used to explore differentially expressed proteins between HCC and adjacent nontumour liver tissue (ANLT). These findings were correlated with clinical outcomes. MATERIALS AND METHODS From 2002 to 2011, tumor and ANLT were collected from patients who underwent liver resection and these samples were later prepared for SELDI-TOF MS. Output data were then used to identify proteins capable of discriminating HCC from ANLT. Proteins from the multivariate analysis were then analyzed to determine prognostic factors and the m/z ratios of these proteins were entered into the ExPASy database to infer potential candidates. RESULTS During the study period, 30 patients had SELDI-TOF MS performed on their HCC and ANLT samples. On multivariate analysis, a panel of four proteins-m/z 5840, m/z 8921, m/z 9961, and m/z 25,872-discriminated HCC from ANLT with an area under the ROC curve of 0.954 (P < 0.001). On prognostic factor assessment, decreased m/z 9961 was significantly associated with the presence of MVI (P = 0.025) and shorter disease-free survival (P = 0.045) in our patients. A potential candidate for this protein was coxsackievirus and adenovirus receptor, isoform 3 (CAR 3/7), which helps maintain tight junction integrity. CONCLUSIONS Using SELDI TOF-MS, we identified a panel of four proteins with excellent discriminative capacity between HCC and ANLT. Of these, m/z 9961 was the only protein significantly associated with a known poor prognostic factor (presence of MVI) and survival (shorter disease-free survival). While loss of CAR 3/7 could lead to MVI, further research is warranted to validate the identity of protein m/z 9961.
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Affiliation(s)
- Steven M Schlichtemeier
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia.
| | - Christopher B Nahm
- Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
| | - Aiqun Xue
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Anthony J Gill
- Department of Anatomical Pathology, Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney NSW and NSW Health Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Ross C Smith
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
| | - Thomas J Hugh
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia; Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
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Harwood FC, Klein Geltink RI, O’Hara BP, Cardone M, Janke L, Finkelstein D, Entin I, Paul L, Houghton PJ, Grosveld GC. ETV7 is an essential component of a rapamycin-insensitive mTOR complex in cancer. SCIENCE ADVANCES 2018; 4:eaar3938. [PMID: 30258985 PMCID: PMC6156121 DOI: 10.1126/sciadv.aar3938] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/03/2018] [Indexed: 05/14/2023]
Abstract
The mechanistic target of rapamycin (mTOR) serine/threonine kinase, a critical regulator of cell proliferation, is frequently deregulated in human cancer. Although rapamycin inhibits the two canonical mTOR complexes, mTORC1 and mTORC2, it often shows minimal benefit as an anticancer drug. This is caused by rapamycin resistance of many different tumors, and we show that a third mTOR complex, mTORC3, contributes to this resistance. The ETS (E26 transformation-specific) transcription factor ETV7 interacts with mTOR in the cytoplasm and assembles mTORC3, which is independent of ETV7's transcriptional activity. This complex exhibits bimodal mTORC1/2 activity but is devoid of crucial mTORC1/2 components. Many human cancers activate mTORC3 at considerable frequency, and tumor cell lines that lose mTORC3 expression become rapamycin-sensitive. We show mTORC3's tumorigenicity in a rhabdomyosarcoma mouse model in which transgenic ETV7 expression accelerates tumor onset and promotes tumor penetrance. Discovery of mTORC3 represents an mTOR paradigm shift and identifies a novel target for anticancer drug development.
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Affiliation(s)
- Franklin C. Harwood
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Brendan P. O’Hara
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Monica Cardone
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Laura Janke
- Department of Veterinary Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Igor Entin
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Leena Paul
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter J. Houghton
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gerard C. Grosveld
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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9
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Alessandrini F, Pezzè L, Menendez D, Resnick MA, Ciribilli Y. ETV7-Mediated DNAJC15 Repression Leads to Doxorubicin Resistance in Breast Cancer Cells. Neoplasia 2018; 20:857-870. [PMID: 30025229 PMCID: PMC6077117 DOI: 10.1016/j.neo.2018.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
Breast cancer treatment often includes Doxorubicin as adjuvant as well as neoadjuvant chemotherapy. Despite its cytotoxicity, cells can develop drug resistance to Doxorubicin. Uncovering pathways and mechanisms involved in drug resistance is an urgent and critical aim for breast cancer research oriented to improve treatment efficacy. Here we show that Doxorubicin and other chemotherapeutic drugs induce the expression of ETV7, a transcriptional repressor member of ETS family of transcription factors. The ETV7 expression led to DNAJC15 down-regulation, a co-chaperone protein whose low expression was previously associated with drug resistance in breast and ovarian cancer. There was a corresponding reduction in Doxorubicin sensitivity of MCF7 and MDA-MB-231 breast cancer cells. We identified the binding site for ETV7 within DNAJC15 promoter and we also found that DNA methylation may be a factor in ETV7-mediated DNAJC15 transcriptional repression. These findings of an inverse correlation between ETV7 and DNAJC15 expression in MCF7 cells in terms of Doxorubicin resistance, correlated well with treatment responses of breast cancer patients with recurrent disease, based on our analyses of reported genome-wide expression arrays. Moreover, we demonstrated that ETV7-mediated Doxorubicin-resistance involves increased Doxorubicin efflux via nuclear pumps, which could be rescued in part by DNAJC15 up-regulation. With this study, we propose a novel role for ETV7 in breast cancer, and we identify DNAJC15 as a new target gene responsible for ETV7-mediated Doxorubicin-resistance. A better understanding of the opposing impacts of Doxorubicin could improve the design of combinatorial adjuvant regimens with the aim of avoiding resistance and relapse.
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Affiliation(s)
- Federica Alessandrini
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy.
| | - Laura Pezzè
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy
| | - Daniel Menendez
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIHES), NIH, Research Triangle Park, NC 27709, USA
| | - Michael A Resnick
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIHES), NIH, Research Triangle Park, NC 27709, USA
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy.
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10
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Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. Molecules 2018; 23:molecules23020328. [PMID: 29401697 PMCID: PMC6017450 DOI: 10.3390/molecules23020328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Butyrophilins (BTNs) are a group of the moonlighting proteins, some members of which are secreted in milk. They constitute a large family of structurally similar type 1 transmembrane proteins from the immunoglobulin superfamily. Although the founding member of this family is related to lactation, participating in the secretion, formation and stabilization of milk fat globules, it may also have a cell surface receptor function. Generally, the BTN family members are known to modulate co-stimulatory responses, T cell selection, differentiation, and cell fate determination. Polymorphism of these genes was shown to be associated with the pathology of several human diseases. Despite their biological significance, structural information on human butyrophilins is rather limited. Based on their remarkable multifunctionality, butyrophilins seem to belong to the category of moonlighting proteins, which are known to contain intrinsically disordered protein regions (IDPRs). However, the disorder status of human BTNs was not systematically investigated as of yet. The goal of this study is to fill this gap and to evaluate peculiarities of intrinsic disorder predisposition of the members of human BTN family, and to find if they have IDPRs that can be attributed to the multifunctionality of these important proteins.
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11
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Caira S, Iannelli A, Sciarrillo R, Picariello G, Renzone G, Scaloni A, Addeo P. Differential representation of liver proteins in obese human subjects suggests novel biomarkers and promising targets for drug development in obesity. J Enzyme Inhib Med Chem 2017; 32:672-682. [PMID: 28274171 PMCID: PMC6009959 DOI: 10.1080/14756366.2017.1292262] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The proteome of liver biopsies from human obese (O) subjects has been compared to those of nonobese (NO) subjects using two-dimensional gel electrophoresis (2-DE). Differentially represented proteins were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based peptide mass fingerprinting (PMF) and nanoflow-liquid chromatography coupled to electrospray-tandem mass spectrometry (nLC-ESI-MS/MS). Overall, 61 gene products common to all of the liver biopsies were identified within 65 spots, among which 25 ones were differently represented between O and NO subjects. In particular, over-representation of short-chain acyl-CoA dehydrogenase, Δ(3,5)-Δ(2,4)dienoyl-CoA isomerase, acetyl-CoA acetyltransferase, glyoxylate reductase/hydroxypyruvate reductase, fructose-biphosphate aldolase B, peroxiredoxin I, protein DJ-1, catalase, α- and β-hemoglobin subunits, 3-mercaptopyruvate S-transferase, calreticulin, aminoacylase 1, phenazine biosynthesis-like domain-containing protein and a form of fatty acid-binding protein, together with downrepresentation of glutamate dehydrogenase, glutathione S-transferase A1, S-adenosylmethionine synthase 1A and a form of apolipoprotein A-I, was associated with the obesity condition. Some of these metabolic enzymes and antioxidant proteins have already been identified as putative diagnostic markers of liver dysfunction in animal models of steatosis or obesity, suggesting additional investigations on their role in these syndromes. Their differential representation in human liver was suggestive of their consideration as obesity human biomarkers and for the development of novel antiobesity drugs.
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Affiliation(s)
- Simonetta Caira
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Antonio Iannelli
- b Département de Chirurgie Digestive , Centre Hospitalier Universitarie de Nice , Nice , France
| | - Rosaria Sciarrillo
- c Dipartimento di Scienze e Tecnologie , Università degli Studi del Sannio , Benevento , Italy
| | | | - Giovanni Renzone
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Andrea Scaloni
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Pietro Addeo
- e Service de Chirurgie Hépatique, Pancréatique, Biliaire et Transplantation, Pôle des Pathologies Digestives, Hépatiques et de la Transplantation, Hôpital de Hautepierre , Université de Strasbourg, Hôpitaux Universitaires de Strasbourg , Strasbourg , France
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12
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Proteomic and metabonomic biomarkers for hepatocellular carcinoma: a comprehensive review. Br J Cancer 2015; 112:1141-56. [PMID: 25826224 PMCID: PMC4385954 DOI: 10.1038/bjc.2015.38] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/04/2014] [Accepted: 12/20/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) ranks third in overall global cancer-related mortality. Symptomatic presentation often means advanced disease where potentially curative treatment options become very limited. Numerous international guidelines propose the routine monitoring of those with the highest risk factors for the condition in order to diagnose potential tumourigenesis early. To aid this, the fields of metabonomic- and proteomic-based biomarker discovery have applied advanced tools to identify early changes in protein and metabolite expression in HCC patients vs controls. With robust validation, it is anticipated that from these candidates will rise a high-performance non-invasive test able to diagnose early HCC and related conditions. This review gathers the numerous markers proposed by studies using mass spectrometry and proton nuclear magnetic resonance spectroscopy and evaluates areas of consistency as well as discordance.
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13
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Chen XG, Xu CS. Proteomic analysis of the regenerating liver following 2/3 partial hepatectomy in rats. Biol Res 2014; 47:59. [PMID: 25723318 PMCID: PMC4335715 DOI: 10.1186/0717-6287-47-59] [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: 07/31/2014] [Accepted: 11/04/2014] [Indexed: 12/16/2022] Open
Abstract
Background Liver regeneration (LR) after 2/3 partial hepatectomy (PH) is one of the most studied models of cell, organ, and tissue regeneration. Although the transcriptional profile analysis of regenerating liver has been carried out by many reserachers, the dynamic protein expression profile during LR has been rarely reported up to date. Therefore, this study aims to detect the global proteomic profile of the regenerating rat liver following 2/3 hepatectomy, thereby gaining some insights into hepatic regeneration mechanism. Results Protein samples extracted from the sham-operated and the regenerating rat livers at 6, 12, 24, 72, 120 and 168 h after PH were separated by IEF/SDS-PAGE and then analyzed by MALDI-TOF/TOF mass spectrometry. Compared to sham-operated groups, there were totally 220 differentially expressed proteins (including 156 up-regulated, 62 down-regulated, and 2 up/down-regulated ones) identified in the regenerating rat livers, and most of them have not been previously related to liver regeneration. According to the expression pattern analysis combined with gene functional analysis, it showed that lipid and carbohydrate metabolism were enhanced at the early phase of LR and continue throughout the regeneration process. Ingenuity Pathway Analysis indicated that YWHAE protein (one of members of the 14-3-3 protein family) was located at the center of pathway networks at all the timepoints after 2/3 hepatectomy under our experimental conditions, maybe suggesting a central role of this protein in regulating liver regeneration. Additionally, we also revealed the role of Cdc42 (cell division cycle 42) in the termination of LR. Conclusions For the first time, our proteomic analysis suggested an important role of YWHAE and pathway mediated by this protein in liver regeneration, which might be helpful in expanding our understanding of LR amd unraveling the mechanisms of LR. Electronic supplementary material The online version of this article (doi:10.1186/0717-6287-47-59) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Guang Chen
- Animal Science and Technology School, Henan University of Science and Technology, Luoyang, Henan Province, 471003, China.
| | - Cun-Shuan Xu
- Key Laboratory for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, 453007, China.
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Taoka M, Morofuji N, Yamauchi Y, Ojima H, Kubota D, Terukina G, Nobe Y, Nakayama H, Takahashi N, Kosuge T, Isobe T, Kondo T. Global PROTOMAP profiling to search for biomarkers of early-recurrent hepatocellular carcinoma. J Proteome Res 2014; 13:4847-58. [PMID: 24967658 DOI: 10.1021/pr500262p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study used global protein expression profiling to search for biomarkers to predict early recurrent hepatocellular carcinoma (HCC). HCC tissues surgically resected from patients with or without recurrence within 2 years (early recurrent) after surgery were compared with adjacent nontumor tissue and with normal liver tissue. We used the PROTOMAP strategy for comparative profiling, which integrates denaturing polyacrylamide gel electrophoresis migratory rates and high-resolution, semiquantitative mass-spectrometry-based identification of in-gel-digested tryptic peptides. PROTOMAP allows examination of global changes in the size, topography, and abundance of proteins in complex tissue samples. This approach identified 8438 unique proteins from 45 708 nonredundant peptides and generated a proteome-wide map of changes in expression and proteolytic events potentially induced by intrinsic apoptotic/necrotic pathways. In the early recurrent HCC tissue, 87 proteins were differentially expressed (≥20-fold) relative to the other tissues, 46 of which were up-regulated or specifically proteolyzed and 41 of which were down-regulated. This data set consisted of proteins that fell into various functional categories, including signal transduction and cell organization and, notably, the major catalytic pathways responsible for liver function, such as the urea cycle and detoxification metabolism. We found that aberrant proteolysis appeared to occur frequently during recurrence of HCC in several key signal transducers, including STAT1 and δ-catenin. Further investigation of these proteins will facilitate the development of novel clinical applications.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University , Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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15
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Chen CP, Haas-Kogan D. Neoplasms of the hepatobiliary system: clinical presentation, molecular pathways and diagnostics. Expert Rev Mol Diagn 2014; 10:883-95. [DOI: 10.1586/erm.10.76] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Comparative proteomic analysis of thiol proteins in the liver after oxidative stress induced by diethylnitrosamine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2528-38. [PMID: 23994225 DOI: 10.1016/j.bbapap.2013.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 07/21/2013] [Accepted: 08/13/2013] [Indexed: 12/18/2022]
Abstract
Conversion of protein -SH groups to disulfides is an early event during protein oxidation, which has prompted great interest in the study of thiol proteins. Chemical carcinogenesis is strongly associated with the formation of reactive oxygen species (ROS). The goal of this study was to detect thiol proteins that are sensitive to ROS generated during diethylnitrosamine (DEN) metabolism in the rat liver. DEN has been widely used to induce experimental hepatocellular carcinoma. We used modified redox-differential gel electrophoresis (redox-DIGE method) and mass spectrometry MALDI-TOF/TOF to identify differential oxidation protein profiles associated with carcinogen exposure. Our analysis revealed a time-dependent increase in the number of oxidized thiol proteins after carcinogen treatment; some of these proteins have antioxidant activity, including thioredoxin, peroxirredoxin 2, peroxiredoxin 6 and glutathione S-transferase alpha-3. According to functional classifications, the identified proteins in our study included chaperones, oxidoreductases, activity isomerases, hydrolases and other protein-binding partners. This study demonstrates that oxidative stress generated by DEN tends to increase gradually through DEN metabolism, causes time-dependent necrosis in the liver and has an oxidative effect on thiol proteins, thereby increasing the number of oxidized thiol proteins. Furthermore, these events occurred during the hepatocarcinogenesis initiation period.
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17
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Megger DA, Bracht T, Kohl M, Ahrens M, Naboulsi W, Weber F, Hoffmann AC, Stephan C, Kuhlmann K, Eisenacher M, Schlaak JF, Baba HA, Meyer HE, Sitek B. Proteomic differences between hepatocellular carcinoma and nontumorous liver tissue investigated by a combined gel-based and label-free quantitative proteomics study. Mol Cell Proteomics 2013; 12:2006-20. [PMID: 23462207 DOI: 10.1074/mcp.m113.028027] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteomics-based clinical studies have been shown to be promising strategies for the discovery of novel biomarkers of a particular disease. Here, we present a study of hepatocellular carcinoma (HCC) that combines complementary two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography (LC-MS)-based approaches of quantitative proteomics. In our proteomic experiments, we analyzed a set of 14 samples (7 × HCC versus 7 × nontumorous liver tissue) with both techniques. Thereby we identified 573 proteins that were differentially expressed between the experimental groups. Among these, only 51 differentially expressed proteins were identified irrespective of the applied approach. Using Western blotting and immunohistochemical analysis the regulation patterns of six selected proteins from the study overlap (inorganic pyrophosphatase 1 (PPA1), tumor necrosis factor type 1 receptor-associated protein 1 (TRAP1), betaine-homocysteine S-methyltransferase 1 (BHMT)) were successfully verified within the same sample set. In addition, the up-regulations of selected proteins from the complements of both approaches (major vault protein (MVP), gelsolin (GSN), chloride intracellular channel protein 1 (CLIC1)) were also reproducible. Within a second independent verification set (n = 33) the altered protein expression levels of major vault protein and betaine-homocysteine S-methyltransferase were further confirmed by Western blots quantitatively analyzed via densitometry. For the other candidates slight but nonsignificant trends were detectable in this independent cohort. Based on these results we assume that major vault protein and betaine-homocysteine S-methyltransferase have the potential to act as diagnostic HCC biomarker candidates that are worth to be followed in further validation studies.
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Affiliation(s)
- Dominik A Megger
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
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18
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Liu H, Zhang J, Wang S, Pang Z, Wang Z, Zhou W, Wu M. Screening of autoantibodies as potential biomarkers for hepatocellular carcinoma by using T7 phase display system. Cancer Epidemiol 2011; 36:82-8. [PMID: 22018955 DOI: 10.1016/j.canep.2011.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 04/04/2011] [Accepted: 04/13/2011] [Indexed: 01/29/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common tumors worldwide. Autoantibodies to tumor-associated proteins in the serum profile, as new biomarkers, may improve the early detection of HCC. METHODS In this study, we interrogated a HCC cDNA T7 phage library for tumor-associated proteins using biopan enrichment techniques with HCC patient and normal sera. The enrichment of tumor-associated proteins after biopanning was tested using plaque assay and immunochemical detection. The putative tumor-associated phage clones were collected for PCR and sequencing analysis. Identities of those selected sequences were revealed through the sequence BLAST program. The identified phage-expressed proteins were then used to develop phage protein ELISA to measure matching autoantibodies using 70 HCC patients, 50 chronic hepatitis patients, and 70 normal serum samples. The logistic regression model and leave-one-out validation were used to evaluate predictive accuracies with a single marker as well as with combined markers. RESULTS Twenty-six phage-displayed proteins have sequence identity with known or putative tumor-associated proteins. Immunochemical reactivity of patient sera with phage-expressed proteins showed that the autoantibodies to phage-expressed protein CENPF, DDX3, HSPA4, HSPA5, VIM, LMNB1, and TP53 had statistical significance in HCC patients. Measurements of the seven autoantibodies combined in a logistic regression model showed that combined measurements of these autoantibodies was more predictive of disease than any single antibody alone, underscoring the importance of identifying multiple potential markers. CONCLUSION Autoantibody in the serum profiling is a promising approach for early detection and diagnosis of HCC. The panel of autoantibodies appears preferable to achieve superior accuracy rather than an autoantibody alone, and may have significant relevance to tumor biology, novel drug development, and immunotherapies.
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Affiliation(s)
- Hui Liu
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
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19
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Albrethsen J, Miller LM, Novikoff PM, Angeletti RH. Gel-based proteomics of liver cancer progression in rat. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1367-76. [DOI: 10.1016/j.bbapap.2011.05.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 05/26/2011] [Accepted: 05/26/2011] [Indexed: 02/08/2023]
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Abstract
To identify Zinc-alpha-2-glycoprotein (ZAG) expression in HCC for serum biomarker, by analyzing the serum proteome of the patients suffering from primary hepatocellular carcinoma (HCC), liver cirrhosis and healthy donors. The serum proteome of the patients from HCC, liver cirrhosis and healthy donors were separated and identified by two-dimensional electrophoresis. The differentially expressed proteins were analyzed by peptide mass fingerprint based on MALDI-TOF-MS and SWISS-PROT or BLAST nr database searching. RT-PCR and Western blotting analysis were used to confirm expression of ZAG in HCC. Five differentially expressed proteins were identified. Albumin, Serotransferrin, CD5 antigen-like precursor ( IgM - associated peptide) were down-regulated in HCC, ZAG and Ig gamma-1 chain C region were up-regulated in HCC. ZAG, a lipid mobilizing factor, is a member of the major histocompatibility complex (MHC) class I family of protein. Five proteins which were found differentially expressed in HCC provided useful information for screening diagnostic tumor markers of human HCC. ZAG might be a novel candidate serum biomarker for HCC early diagnosis.
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21
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Marimuthu A, O’Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole RN, Harsha H, Pandey A. A comprehensive map of the human urinary proteome. J Proteome Res 2011; 10:2734-43. [PMID: 21500864 PMCID: PMC4213861 DOI: 10.1021/pr2003038] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the human urinary proteome has the potential to offer significant insights into normal physiology as well as disease pathology. The information obtained from such studies could be applied to the diagnosis of various diseases. The high sensitivity, resolution, and mass accuracy of the latest generation of mass spectrometers provides an opportunity to accurately catalog the proteins present in human urine, including those present at low levels. To this end, we carried out a comprehensive analysis of human urinary proteome from healthy individuals using high-resolution Fourier transform mass spectrometry. Importantly, we used the Orbitrap for detecting ions in both MS (resolution 60 000) and MS/MS (resolution 15 000) modes. To increase the depth of our analysis, we characterized both unfractionated as well as lectin-enriched proteins in our experiments. In all, we identified 1,823 proteins with less than 1% false discovery rate, of which 671 proteins have not previously been reported as constituents of human urine. This data set should serve as a comprehensive reference list for future studies aimed at identification and characterization of urinary biomarkers for various diseases.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Manipal University, Manipal 576104, Karnataka, India
| | - Robert N. O’Meally
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, Karnataka, India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Dhanashree S. Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- School of Biotechnology, Amrita University, Kollam 690525, Kerala, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Rakesh Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560006, Karnataka, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- School of Biotechnology, Amrita University, Kollam 690525, Kerala, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560006, Karnataka, India
| | | | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - H.C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
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22
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The application of SELDI-TOF-MS in clinical diagnosis of cancers. J Biomed Biotechnol 2011; 2011:245821. [PMID: 21687541 PMCID: PMC3114543 DOI: 10.1155/2011/245821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/30/2011] [Indexed: 12/24/2022] Open
Abstract
Cancer diagnosis is important, and the early diagnosis of cancers could predict a more successful treatment. The proteomic studies emerged to be useful in combined analyses of samples from patients and provide more accurate diagnosis when compared to the single-factor-based diagnosis. In recent years, cancer detection with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS) is flourishing and brought significant progress in this area. This paper summarizes some recent results with this technique for cancer diagnosis.
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Khalil AA, Kabapy NF, Deraz SF, Smith C. Heat shock proteins in oncology: diagnostic biomarkers or therapeutic targets? Biochim Biophys Acta Rev Cancer 2011; 1816:89-104. [PMID: 21605630 DOI: 10.1016/j.bbcan.2011.05.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Revised: 05/04/2011] [Accepted: 05/06/2011] [Indexed: 02/08/2023]
Abstract
Heat shock proteins (HSP) are a family of proteins induced in cells exposed to different insults. This induction of HSPs allows cells to survive stress conditions. Mammalian HSPs have been classified into six families according to their molecular size: HSP100, HSP90, HSP70, HSP60, HSP40 and small HSPs (15 to 30kDa) including HSP27. These proteins act as molecular chaperones either helping in the refolding of misfolded proteins or assisting in their elimination if they become irreversibly damaged. In recent years, proteomic studies have characterized several different HSPs in various tumor types which may be putative clinical biomarkers or molecular targets for cancer therapy. This has led to the development of a series of molecules capable of inhibiting HSPs. Numerous studies speculated that over-expression of HSP is in part responsible for resistance to many anti-tumor agents and chemotherapeutics. Hence, from a pharmacological point of view, the co-administration of HSP inhibitors together with other anti-tumor agents is of major importance in overcoming therapeutic resistance. In this review, we provide an overview of the current status of HSPs in autoimmune, cardiovascular, and neurodegenerative diseases with special emphasis on cancer.
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Affiliation(s)
- Ashraf A Khalil
- Department of Protein Technology, Institute of Genetic Engineering and Biotechnology, Mubarak City for Scientific Research, New Borg Elarab, Alexandria, Egypt.
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24
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Cutrera J, Dibra D, Xia X, Hasan A, Reed S, Li S. Discovery of a linear peptide for improving tumor targeting of gene products and treatment of distal tumors by IL-12 gene therapy. Mol Ther 2011; 19:1468-77. [PMID: 21386825 DOI: 10.1038/mt.2011.38] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Like many effective therapeutics, interleukin-12 (IL-12) therapy often causes side effects. Tumor targeted delivery may improve the efficacy and decrease the toxicity of systemic IL-12 treatments. In this study, a novel targeting approach was investigated. A secreted alkaline phosphatase (SEAP) reporter gene-based screening process was used to identify a mini-peptide which can be produced in vivo to target gene products to tumors. The coding region for the best peptide was inserted into an IL-12 gene to determine the antitumor efficacy. Affinity chromatography, mass spectrometry analysis, and binding studies were used to identify a receptor for this peptide. We discovered that the linear peptide VNTANST increased the tumor accumulation of the reporter gene products in five independent tumor models including one human xenogeneic model. The product from VNTANST-IL-12 fusion gene therapy increased accumulation of IL-12 in the tumor environment, and in three tumor models, VNTANST-IL-12 gene therapy inhibited distal tumor growth. In a spontaneous lung metastasis model, inhibition of metastatic tumor growth was improved compared to wild-type IL-12 gene therapy, and in a squamous cell carcinoma model, toxic liver lesions were reduced. The receptor for VNTANST was identified as vimentin. These results show the promise of using VNTANST to improve IL-12 treatments.
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Affiliation(s)
- Jeffry Cutrera
- Department of Pediatrics, MD Anderson Cancer Center, Houston, Texas, USA
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25
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Liu Z, Ma Y, Yang J, Qin H. Upregulated and Downregulated Proteins in Hepatocellular Carcinoma: A Systematic Review of Proteomic Profiling Studies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:61-71. [PMID: 20726783 DOI: 10.1089/omi.2010.0061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Zhihua Liu
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanlei Ma
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jianjun Yang
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Huanlong Qin
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
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26
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Quantitative proteomic analyses of influenza virus-infected cultured human lung cells. J Virol 2010; 84:10888-906. [PMID: 20702633 DOI: 10.1128/jvi.00431-10] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Because they are obligate intracellular parasites, all viruses are exclusively and intimately dependent upon host cells for replication. Viruses, in turn, induce profound changes within cells, including apoptosis, morphological changes, and activation of signaling pathways. Many of these alterations have been analyzed by gene arrays, which measure the cellular "transcriptome." Until recently, it has not been possible to extend comparable types of studies to globally examine all the host cellular proteins, which are the actual effector molecules. We have used stable isotope labeling by amino acids in cell culture (SILAC), combined with high-throughput two-dimensional (2-D) high-performance liquid chromatography (HPLC)/mass spectrometry, to determine quantitative differences in host proteins after infection of human lung A549 cells with human influenza virus A/PR/8/34 (H1N1) for 24 h. Of the 4,689 identified and measured cytosolic protein pairs, 127 were significantly upregulated at >95% confidence, 153 were significantly downregulated at >95% confidence, and a total of 87 proteins were upregulated or downregulated more than 5-fold at >99% confidence. Gene ontology and pathway analyses indicated differentially regulated proteins and included those involved in host cell immunity and antigen presentation, cell adhesion, metabolism, protein function, signal transduction, and transcription pathways.
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27
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Proteomic analysis of regenerating mouse liver following 50% partial hepatectomy. Proteome Sci 2009; 7:48. [PMID: 20040084 PMCID: PMC2813229 DOI: 10.1186/1477-5956-7-48] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/29/2009] [Indexed: 12/29/2022] Open
Abstract
Background Although 70% (or 2/3) partial hepatectomy (PH) is the most studied model for liver regeneration, the hepatic protein expression profile associated with lower volume liver resection (such as 50% PH) has not yet been reported. Therefore, the aim of this study was to determine the global protein expression profile of the regenerating mouse liver following 50% PH by differential proteomics, and thereby gaining some insights into the hepatic regeneration mechanism(s) under this milder but clinically more relevant condition. Results Proteins from sham-operated mouse livers and livers regenerating for 24 h after 50% PH were separated by SDS-PAGE and analyzed by nanoUPLC-Q-Tof mass spectrometry. Compared to sham-operated group, there were totally 87 differentially expressed proteins (with 50 up-regulated and 37 down-regulated ones) identified in the regenerating mouse livers, most of which have not been previously related to liver regeneration. Remarkably, over 25 differentially expressed proteins were located at mitochondria. Several of the mitochondria-resident proteins which play important roles in citric acid cycle, oxidative phosphorylation and ATP production were found to be down-regulated, consistent with the recently-proposed model in which the reduction of ATP content in the remnant liver gives rise to early stress signals that contribute to the onset of liver regeneration. Pathway analysis revealed a central role of c-Myc in the regulation of liver regeneration. Conclusions Our study provides novel evidence for mitochondria as a pivotal organelle that is connected to liver regeneration, and lays the foundation for further studies on key factors and pathways involved in liver regeneration following 50% PH, a condition frequently used for partial liver transplantation and conservative liver resection.
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