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Cho HY, Lee JE, Park KH, Choi BY, Lee MJ, Jeong DE, Shin S. Identification and characterization of plasma proteins associated with intra-amniotic inflammation and/or infection in women with preterm labor. Sci Rep 2024; 14:14654. [PMID: 38918423 PMCID: PMC11199617 DOI: 10.1038/s41598-024-65616-x] [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: 01/17/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
This study aimed to identify plasma proteins that could serve as potential biomarkers for microbial invasion of the amniotic cavity (MIAC) or intra-amniotic inflammation (IAI) in women with preterm labor (PTL). A retrospective cohort comprised singleton pregnant women with PTL (24-34 weeks) who underwent amniocentesis. Pooled plasma samples were analyzed by label-free liquid chromatography-tandem mass spectrometry for proteome profiling in a nested case-control study (concomitant MIAC/IAI cases vs. non-MIAC/IAI controls [n = 10 per group]). Eight target proteins associated with MIAC/IAI were further verified by immunoassays in a large cohort (n = 230). Shotgun proteomic analysis revealed 133 differentially expressed proteins (fold change > 1.5, P < 0.05) in the plasma of MIAC/IAI cases. Further quantification confirmed that the levels of AFP were higher and those of kallistatin and TGFBI were lower in the plasma of women with MIAC and that the levels of kallistatin and TGFBI were lower in the plasma of women with IAI than in those without these conditions. The area under the curves of plasma AFP, kallistatin, and TGFBI ranged within 0.67-0.81 with respect to each endpoint. In summary, plasma AFP, kallistatin, and TGFBI may represent valuable non-invasive biomarkers for predicting MIAC or IAI in women with PTL.
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Affiliation(s)
- Hee Young Cho
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Ji Eun Lee
- Chemical & Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea.
| | - Bo Young Choi
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea
| | - Min Jung Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea
| | - Da Eun Jeong
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-Ro 173 Beon-Gil, Bundang-Gu, Seongnam, 463-707, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Boramae Hospital, Seoul, Korea
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Song F, Dai Q, Grimm MO, Steinbach D. The Antithetic Roles of IQGAP2 and IQGAP3 in Cancers. Cancers (Basel) 2023; 15:cancers15041115. [PMID: 36831467 PMCID: PMC9953781 DOI: 10.3390/cancers15041115] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The scaffold protein family of IQ motif-containing GTPase-activating proteins (IQGAP1, 2, and 3) share a high degree of homology and comprise six functional domains. IQGAPs bind and regulate the cytoskeleton, interact with MAP kinases and calmodulin, and have GTPase-related activity, as well as a RasGAP domain. Thus, IQGAPs regulate multiple cellular processes and pathways, affecting cell division, growth, cell-cell interactions, migration, and invasion. In the past decade, significant evidence on the function of IQGAPs in signal transduction during carcinogenesis has emerged. Compared with IQGAP1, IQGAP2 and IQGAP3 were less analyzed. In this review, we summarize the different signaling pathways affected by IQGAP2 and IQGAP3, and the antithetic roles of IQGAP2 and IQGAP3 in different types of cancer. IQGAP2 expression is reduced and plays a tumor suppressor role in most solid cancer types, while IQGAP3 is overexpressed and acts as an oncogene. In lymphoma, for example, IQGAPs have partially opposite functions. There is considerable evidence that IQGAPs regulate a multitude of pathways to modulate cancer processes and chemoresistance, but some questions, such as how they trigger this signaling, through which domains, and why they play opposite roles on the same pathways, are still unanswered.
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Affiliation(s)
- Fei Song
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
| | - Qingqing Dai
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, 07740 Jena, Germany
| | - Marc-Oliver Grimm
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
| | - Daniel Steinbach
- Department of Urology, Jena University Hospital, 07740 Jena, Germany
- Correspondence:
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3
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Lee JE, Park KH, Kim HJ, Kim YM, Choi JW, Shin S, Lee KN. Proteomic identification of novel plasma biomarkers associated with spontaneous preterm birth in women with preterm labor without infection/inflammation. PLoS One 2021; 16:e0259265. [PMID: 34710180 PMCID: PMC8553083 DOI: 10.1371/journal.pone.0259265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
Objective We sought to identify plasma biomarkers associated with spontaneous preterm birth (SPTB, delivery within 21 days of sampling) in women with preterm labor (PTL) without intra-amniotic infection/inflammation (IAI) using label-free quantitative proteomic analysis, as well as to elucidate specific protein pathways involved in these cases. Methods This was a retrospective cohort study comprising 104 singleton pregnant women with PTL (24–32 weeks) who underwent amniocentesis and demonstrated no evidence of IAI. Analysis of pooled plasma samples collected from SPTB cases and term birth (TB) controls (n = 10 for each group) was performed using label-free quantitative mass spectrometry for proteome profiling in a nested case-control study design. Eight candidate proteins of interest were validated by ELISA-based assay and a clot-based assay in the total cohort. Results Ninety-one proteins were differentially expressed (P < 0.05) in plasma samples obtained from SPTB cases, of which 53 (58.2%) were upregulated and 38 (41.8%) were downregulated when compared to TD controls. A validation study confirmed that plasma from women who delivered spontaneously within 21 days of sampling contained significantly higher levels of coagulation factor Ⅴ and lower levels of S100 calcium binding protein A9 (S100A9), especially the former which was independent of baseline variables. The top-ranked pathways related to the 91 differentially expressed proteins were liver-X-receptor/retinoid X receptor (RXR) activation, acute phase response signaling, farnesoid X receptor/RXR activation, coagulation system, and complement system. Conclusions Proteomic analyses in this study identified potential novel biomarkers (i.e., coagulation factor V and S100A9) and potential protein pathways in plasma associated with SPTB in the absence of IAI in women with PTL. The present findings provide novel insights into the molecular pathogenesis and therapeutic targets specific for idiopathic SPTB.
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Affiliation(s)
- Ji Eun Lee
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- * E-mail:
| | - Hyeon Ji Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yu Mi Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Ji-Woong Choi
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Boramae Hospital, Seoul, Korea
| | - Kyong-No Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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Abstract
The uptake of calcium into and extrusion of calcium from the mitochondrial matrix is a fundamental biological process that has critical effects on cellular metabolism, signaling, and survival. Disruption of mitochondrial calcium (mCa2+) cycling is implicated in numerous acquired diseases such as heart failure, stroke, neurodegeneration, diabetes, and cancer, and is genetically linked to several inherited neuromuscular disorders. Understanding the mechanisms responsible for mCa2+ exchange therefore holds great promise for the treatment of these diseases. The past decade has seen the genetic identification of many of the key proteins that mediate mitochondrial calcium uptake and efflux. Here, we present an overview of the phenomenon of mCa2+ transport, and a comprehensive examination of the molecular machinery that mediates calcium flux across the inner mitochondrial membrane: the mitochondrial uniporter complex (consisting of MCU, EMRE, MICU1, MICU2, MICU3, MCUB, and MCUR1), NCLX, LETM1, the mitochondrial ryanodine receptor, and the mitochondrial permeability transition pore. We then consider the physiological implications of mCa2+ flux and evaluate how alterations in mCa2+ homeostasis contribute to human disease. This review concludes by highlighting opportunities and challenges for therapeutic intervention in pathologies characterized by aberrant mCa2+ handling and by summarizing critical unanswered questions regarding the biology of mCa2+ flux.
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Affiliation(s)
- Joanne F Garbincius
- Center for Translational Medicine, Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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Xing X, Yuan H, Liu H, Tan X, Zhao B, Wang Y, Ouyang J, Lin M, Liu X, Huang A. Quantitative Secretome Analysis Reveals Clinical Values of Carbonic Anhydrase II in Hepatocellular Carcinoma. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:94-107. [PMID: 33662630 PMCID: PMC8498920 DOI: 10.1016/j.gpb.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/15/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Early detection and intervention are key strategies to reduce mortality, increase long-term survival, and improve the therapeutic effects of hepatocellular carcinoma (HCC) patients. Herein, the isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic strategy was used to study the secretomes in conditioned media from HCC cancerous tissues, surrounding noncancerous tissues, and distal noncancerous tissues to identify diagnostic and prognostic biomarkers for HCC. In total, 22 and 49 dysregulated secretory proteins were identified in the cancerous and surrounding noncancerous tissues, respectively, compared with the distal noncancerous tissues. Among these proteins, carbonic anhydrase II (CA2) was identified to be significantly upregulated in the secretome of cancerous tissues; correspondingly, the serum concentrations of CA2 were remarkably increased in HCC patients compared with that in normal populations. Interestingly, a significant increase of serum CA2 in recurrent HCC patients after radical resection was also confirmed compared with HCC patients without recurrence, and the serum level of CA2 could act as an independent prognostic factor for time to recurrence and overall survival. Regarding the mechanism, the secreted CA2 enhances the migration and invasion of HCC cells by activating the epithelial mesenchymal transition pathway. Taken together, this study identified a novel biomarker for HCC diagnosis and prognosis, and provided a valuable resource of HCC secretome for investigating serological biomarkers.
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Affiliation(s)
- Xiaohua Xing
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Hui Yuan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Hongzhi Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xionghong Tan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Minjie Lin
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xiaolong Liu
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.
| | - Aimin Huang
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China.
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Shin SJ, Nam Y, Park YH, Kim MJ, Lee E, Jeon SG, Bae BS, Seo J, Shim SL, Kim JS, Han CK, Kim S, Lee YY, Moon M. Therapeutic effects of non-saponin fraction with rich polysaccharide from Korean red ginseng on aging and Alzheimer's disease. Free Radic Biol Med 2021; 164:233-248. [PMID: 33422674 DOI: 10.1016/j.freeradbiomed.2020.12.454] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022]
Abstract
Biological aging provokes morbidity and several functional declines, causing older adults more susceptible to a variety of diseases than younger adults. In particular, aging is a major risk factor contributing to non-communicable diseases, such as neurodegenerative disorders. Alzheimer's disease (AD) is an aging-related neurodegenerative disease that is characterized by cognitive deficits and the formation of amyloid plaques formed by the accumulation of amyloid-β (Aβ) peptides. Non-saponin fraction with rich polysaccharide (NFP) from red ginseng, the largest fraction of the components of red ginseng, perform many biological activities. However, it has not been clarified whether the NFP from Korean red ginseng (KRG) has beneficial effects in the aging and AD. First, proteomics analysis was performed in aged brain to identify the effect of NFP on protein changes, and we confirmed that NFP induced changes in proteins related to the neuroprotective- and neurogenic-effects. Next, we investigated (1) the effects of NFP on AD pathologies, such as Aβ deposition, neuroinflammation, neurodegeneration, mitochondrial dysfunction, and impaired adult hippocampal neurogenesis (AHN), in 5XFAD transgenic mouse model of AD using immunostaining; (2) the effect of NFP on Aβ-mediated mitochondrial respiration deficiency in HT22 mouse hippocampal neuronal cells (HT22) using Seahorse XFp analysis; (3) the effect of NFP on cell proliferation using WST-1 analysis; and (4) the effect of NFP on Aβ-induced cognitive dysfunction in 5XFAD mouse model of AD using Y-maze test. Histological analysis indicated that NFP significantly alleviated the accumulation of Aβ, neuroinflammation, neuronal loss, and mitochondrial dysfunction in the subiculum of 5XFAD mouse model of AD. In addition, NFP treatment ameliorated mitochondrial deficits in Aβ-treated HT22 cells. Moreover, NFP treatment significantly increased the AHN and neuritogenesis of neural stem cells in both healthy and AD brains. Furthermore, NFP significantly increased cell proliferation in the HT22 cells. Finally, NFP administration significantly enhanced and restored the cognitive function of healthy and AD mice, respectively. Taken together, NFP treatment demonstrated changes in proteins involved in central nervous system organization/maintenance in aged brain and ameliorates AD pathology. Collectively, our findings suggest that NFP from KRG could be a potential therapeutic candidate for aging and AD treatments.
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Affiliation(s)
- Soo Jung Shin
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Yunkwon Nam
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Yong Ho Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Min-Jeong Kim
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Eunbeen Lee
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Seong Gak Jeon
- Department of Neural Development and Disease, Korea Brain Research Institute (KBRI), Daegu, 41068, Republic of Korea
| | - Bong-Seok Bae
- The Korean Ginseng Research Institute, Korea Ginseng Corporation, Gajeong-ro 30, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea
| | - Jiho Seo
- The Korean Ginseng Research Institute, Korea Ginseng Corporation, Gajeong-ro 30, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea
| | - Sung-Lye Shim
- The Korean Ginseng Research Institute, Korea Ginseng Corporation, Gajeong-ro 30, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea
| | - Jong-Seok Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Chang-Kyun Han
- The Korean Ginseng Research Institute, Korea Ginseng Corporation, Gajeong-ro 30, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea
| | - Sujin Kim
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, Daejeon, 35365, Republic of Korea.
| | - Yong Yook Lee
- The Korean Ginseng Research Institute, Korea Ginseng Corporation, Gajeong-ro 30, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea.
| | - Minho Moon
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, Daejeon, 35365, Republic of Korea.
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Hong S, Lee JE, Kim YM, Park Y, Choi JW, Park KH. Identifying potential biomarkers related to pre-term delivery by proteomic analysis of amniotic fluid. Sci Rep 2020; 10:19648. [PMID: 33184413 PMCID: PMC7665029 DOI: 10.1038/s41598-020-76748-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
We sought to identify biomarkers in the amniotic fluid (AF) and specific signaling pathways related to spontaneous preterm delivery (SPTD, < 34 weeks) in women with preterm labor (PTL) without intra-uterine infection/inflammation (IUI). This was a retrospective cohort study of a total of 139 PTL women with singleton gestation (24 + 0 to 32 + 6 weeks) who underwent amniocentesis and who displayed no evidence of IUI. A nested case-control was conducted using pooled AF samples (n = 20) analyzed via label-free liquid chromatography-tandem mass spectrometry. In the total cohort, an ELISA validation study was performed for seven candidate proteins of interest. Proteomic analysis identified 77 differentially expressed proteins (DEPs, P < 0.05) in the AF from SPTD cases compared to term delivery controls. ELISA validation confirmed that women who had an SPTD before 34 weeks had significantly independently lower levels of VEGFR-1 and higher levels of lipocalin-2 and the Fc fragment of IgG binding protein in the AF. Five principle pathways associated with the 77 DEPs were identified, including glycolysis, gluconeogenesis, and iron homeostasis. The proteomic analysis data of AFs from women with PTL identified several novel biomarkers and specific protein pathways related to SPTD in the absence of IUI.
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Affiliation(s)
- Subeen Hong
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea
| | - Yu Mi Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, 463-707, Korea
| | - Yehyon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, 463-707, Korea
| | - Ji-Woong Choi
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Korea
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, 463-707, Korea.
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Liu Q, Hua S, Wang X, Chen F, Gou S. The introduction of immunosuppressor (TDO inhibitor) significantly improved the efficacy of irinotecan in treating hepatocellular carcinoma. Cancer Immunol Immunother 2020; 70:497-508. [PMID: 32840656 DOI: 10.1007/s00262-020-02697-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022]
Abstract
As TDO inhibitors can improve the efficacy of tumor chemotherapeutics, two TDO-targeted conjugates consisting of irinotecan (Ir) and a TDO inhibitor unit were designed and prepared to reverse tumor immune suppression, which could remarkably enhance antitumor activity of Ir by boosting cellular uptakes against TDO overexpressed HepG2 cancer cells. In vitro mechanistic studies demonstrated that compound PVIS-Ir and PVIG-Ir could arrest cell cycle at G2 phase and induce cell apoptosis by mitochondrial apoptotic pathway. Furthermore, compound PVIS-Ir could effectively inhibit TDO protein expression via releasing a TDO inhibitor derivative, which could also completely embed in TDO protein pocket. Further mechanism study indicated that PVIS-Ir could block kynurenine production and deactivate aryl hydrocarbon receptor (AHR), resulting in T-cell activation and proliferation. In vivo studies confirmed that PVIS-Ir could improve tumor immune microenvironment in a murine model. This combinational strategy of chemotherapy and immunotherapy can be a promising way in the treatment of hepatocellular carcinoma. Conjugates obtained by combining an immune checkpoint TDO inhibitor with irinotecan via different linkers could improve tumor immune microenvironment by inhibiting the TDO enzyme expression to block kynurenine production and induce HepG2 cancer cell apoptosis via DNA damage through releasing a TDO inhibitor and irinotecan in cancer cells.
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Affiliation(s)
- Qingqing Liu
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Shixian Hua
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Xinyi Wang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Feihong Chen
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China. .,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Shaohua Gou
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China. .,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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9
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Biological Effects of Korean Red Ginseng Polysaccharides in Aged Rat Using Global Proteomic Approach. Molecules 2020; 25:molecules25133019. [PMID: 32630349 PMCID: PMC7412055 DOI: 10.3390/molecules25133019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/20/2020] [Accepted: 06/29/2020] [Indexed: 01/07/2023] Open
Abstract
Much has been written on the physiological benefits of Korean Red Ginseng (KRG). Among its various components, ginsenosides have been widely investigated for their various pharmacological effects. However, polysaccharides are a major KRG component that has not received scrutiny similar to that of ginsenosides. The present study aims to fill that gap in the existing literature and to investigate the possible functions of polysaccharide in KRG. The researchers evaluated proteomic changes in non-saponin fractions with rich polysaccharides (NFP) in KRG. Based on the serum analysis, proteomics analysis of the liver and the spleen was additionally conducted to identify related functions. We validated the suggested functions of NFP with the galactosamine-induced liver injury model and the cyclophosphamide-induced immunosuppression model. Then, we evaluated the antimetastatic potential of NFP in the lungs. Further proteomics analysis of the spleen and liver after ingestion confirmed functions related to immunity, cancer, hepatoprotection, and others. Then, we validated the suggested corresponding functions of the NFP in vivo model. NFP showed immune-enhancing effects, inhibited melanoma cell metastasis in the lung, and decreased liver damage. The results show that using the proteomic approach uncovers the potential effects of polysaccharides in KRG, which include enhancing the immune system and protecting the liver.
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Lin X, Huang Y, Sun Y, Tan X, Ouyang J, Zhao B, Wang Y, Xing X, Liu J. 4E-BP1 Thr46 Phosphorylation Association with Poor Prognosis in Quantitative Phosphoproteomics of Portal Vein Tumor Thrombus Revealed that 4E-BP1Thr46 Phosphorylation is Associated with Poor Prognosis in HCC. Cancer Manag Res 2020; 12:103-115. [PMID: 32021427 PMCID: PMC6954833 DOI: 10.2147/cmar.s230849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/30/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose Early formation of portal vein tumor thrombosis (PVTT) is a key characteristic of hepatocellular carcinoma (HCC) metastasis, but to date, the aetiology of PVTT in HCC metastasis is largely unknown. We aim to find highly sensitive and specific biomarkers for the prediction of HCC prognosis. Patients and methods We used isobaric tags for relative and absolute quantitation (iTRAQ) based quantitative phosphoproteomics approach to investigate the molecular signatures of the HCC with PVTT in primary HCC tissues, surrounding non-cancerous tissues and PVTT tissues. The different proteome profiles in three groups were investigated and might reveal different underlying molecular mechanisms. Results In total, we identified 1745 phosphoproteins with 2724 phosphopeptides and 4594 phosphorylation sites in three groups. Among these phosphoproteins, 80 phosphoproteins were dysregulated in PVTT/Pan group, 51 phosphoproteins were dysregulated in HCC/Pan group, and 10 phosphoproteins were dysregulated in PVTT/HCC group. Furthermore, the phosphorylation of 4E-BP1 was elevated in HCC tissues and PVTT tissues in comparison with surrounding non-cancerous tissues, and the elevated fold change of phosphorylation level was higher than that in expression level of 4E-BP1. The further IHC analysis in acohort of 20 HCC tissues showed that the phosphorylation of 4E-BP1 on Thr46 might be closely related to HCC prognosis. Conclusion The high phosphorylation level of 4E-BP1Thr46 might serve as a biomarker for the diagnosis of early recurrence and metastasis of HCC.
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Affiliation(s)
- Xincong Lin
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China.,The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Yao Huang
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China.,The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Ying Sun
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Xionghong Tan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Xiaohua Xing
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China.,The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Jingfeng Liu
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China.,The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
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11
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Lee J, Lee JE, Choi JW, Han MH, Seong SY, Park KH, Park JW. Proteomic Analysis of Amniotic Fluid Proteins for Predicting the Outcome of Emergency Cerclage in Women with Cervical Insufficiency. Reprod Sci 2020; 27:1318-1329. [PMID: 32046453 DOI: 10.1007/s43032-019-00110-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022]
Abstract
We aimed to identify novel biomarkers in amniotic fluid (AF) that predict the outcome of emergency cerclage in women with cervical insufficiency. This retrospective cohort study included 40 singleton pregnant women who received emergency cerclage for cervical insufficiency (17-25 weeks) and underwent amniocentesis. Label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify AF proteins in pooled samples (n = 16) using a nested case-control approach. The six candidate biomarkers of interest were validated by enzyme-linked immunosorbent assays (ELISA) in the final cohort (n = 40). The differentially expressed proteins (DEPs) were analyzed by pathway analysis software. The primary outcome measure was failure of emergency cerclage [defined as spontaneous preterm delivery (SPTD) at < 34 weeks of gestation after cerclage placement]. Sixty-eight proteins were differentially expressed (P < 0.001) in AF from SPTD cases and near-term controls, of which 44 (64.7%) were upregulated and 24 (35.3%) were downregulated. Validation by ELISA confirmed that AF from women with cerclage failure contained significantly higher levels of myeloperoxidase, lactoferrin, glucose-6-phosphate isomerase, lipocalin-2, and lymphocyte cytosolic protein 1, the first four of which were independent of cervical dilatation at presentation. The five pathways with the most differentially regulated proteins were actin cytoskeleton signaling, acute phase response signaling, ILK signaling, glycolysis, and gluconeogenesis. Proteomic analyses of AF in this study identified DEPs and specific protein pathways related to poor prognosis after emergency cerclage for cervical insufficiency. Four novel independent biomarkers in AF for cerclage failure have been identified using proteomics.
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Affiliation(s)
- JoonHo Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Yonsei University Health System, Seoul, South Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Ji-Woong Choi
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Mi-Hee Han
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Seung-Yong Seong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyo Hoon Park
- Departments of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea.
| | - Jeong Woo Park
- Departments of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea.
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12
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Hua S, Wang X, Chen F, Gou S. Novel conjugates with dual suppression of glutathione S-transferases and tryptophan-2,3-dioxygenase activities for improving hepatocellular carcinoma therapy. Bioorg Chem 2019; 92:103191. [PMID: 31445192 DOI: 10.1016/j.bioorg.2019.103191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/01/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022]
Abstract
Tryptophan-2,3-dioxygenase (TDO) is an immune checkpoint enzyme expressed in human tumors and involved in immune evasion and tumor tolerance. While glutathione S-transferases (GSTs) are pharmacological targets for several cancer. Here we demonstrated the utility of NBDHEX (GSTs inhibitor) and TDO inhibitor by the combinatorial linker design. Two novel conjugates with different linkers were prepared to reverse tumor immune suppression. The conjugates displayed significant antitumor activity against TDO and GSTs expression of HepG2 cancer cells. Further study indicated that compound 4 could induce higher apoptotic effect than its mother compounds via a mitochondrial-dependent pathway, simultaneously more effective to inhibit TDO and GSTs protein expression. Further study indicated that 4 could decrease the production of kynurenine and deactivate aryl hydrocarbon receptor (AHR), leading to CD3+T-cell activation and proliferation to involve in antitumor immune response.
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Affiliation(s)
- Shixian Hua
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China; Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xinyi Wang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China; Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Feihong Chen
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China; Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Shaohua Gou
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, China; Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
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13
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Li N, Liu T, Li H, Zhang L, Chu L, Meng Q, Qiao Q, Han W, Zhang J, Guo M, Zhao J. ILF2 promotes anchorage independence through direct regulation of PTEN. Oncol Lett 2019; 18:1689-1696. [PMID: 31423236 PMCID: PMC6614677 DOI: 10.3892/ol.2019.10510] [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] [Received: 05/17/2018] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Anoikis is a specific form of programmed cell death induced by loss of contact between cells and extracellular matrices or other cells. Only tumor cells that are resistant to anoikis can survive in the state of detachment from the primary tissue during the early stages of metastasis. The ability to resist anoikis is crucial for cancer cell metastasis. ILF2 is a proto-oncogene previously studied in glioma, NSCLC, esophageal cancer and pancreatic ductal carcinoma. The results from the present study revealed that the transcription factor interleukin enhancer-binding factor 2 (ILF2) was highly expressed in non-small cell lung cancer (NSCLC) cell lines compared with in normal cell lines. ChIP and luciferase reporter gene assays demonstrated that ILF2 inhibited the expression level of the tumor suppressor gene phosphatase and tensin homolog (PTEN) by directly binding to its upstream regulatory region. Furthermore, the results from the detection of cell adhesion and apoptosis in cell suspension culture demonstrated that this mechanism enabled NSCLC cells to reduce adherence to the matrix and to survive in this abnormal state. These results suggested that ILF2 may promote the anchorage-independence of NSCLC cells through the suppression of PTEN.
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Affiliation(s)
- Na Li
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Tao Liu
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Hui Li
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Lifang Zhang
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Liping Chu
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Qingge Meng
- Department of Internal Medicine, Xingtai Medical College, The Third Affiliated Hospital of Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Qinzeng Qiao
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Weikun Han
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Junhui Zhang
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Minying Guo
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Jia Zhao
- Department of Internal Medicine, The Third Affiliated Hospital of Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
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14
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ANXA2 Tyr23 and FLNA Ser2152 phosphorylation associate with poor prognosis in hepatic carcinoma revealed by quantitative phosphoproteomics analysis. J Proteomics 2019; 200:111-122. [PMID: 30951906 DOI: 10.1016/j.jprot.2019.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/15/2019] [Accepted: 03/31/2019] [Indexed: 02/06/2023]
Abstract
Hepatoma is one of the most common malignant tumors, and most patients have very poor prognosis. Early prediction and intervention of the hepatoma recurrence/metastasis are the most effective way to improve the patients' clinical outcomes. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) based quantitative phospho-proteomics approach to identify biomarkers associated with hepatoma recurrence/metastasis in hepatoma cell lines with increasing metastasis ability. In total, 75 phosphorylated peptides corresponding to 60 phosphoproteins were significantly dysregulated and the participated biological processes of these phosphoproteins were tightly associated with tumor metastasis. Further signaling pathway analysis revealed that key signaling pathways which play crucial roles in cancer metastasis have been significantly over activated in the highly metastatic cells. Furthermore, the phosphorylation of FLNASer2152 and ANXA2Tyr23 were validated to be significantly up regulated in the high-metastatic cells comparing with the low-metastatic cells. By further investigation the clinical significance of the phosphorylation of FLNASer2152 and ANXA2Tyr23 in large-scale clinical samples, revealed that the over phosphorylation of FLNASer2152 and ANXA2Tyr23 were associated with poor prognosis and might be potential prognostic biomarkers for the primary hepatoma. When FLNASer2152 combined with ANXA2Tyr23, it had a better prognostic value for both OS and TTR.
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15
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Li Y, Tran Q, Shrestha R, Piao L, Park S, Park J, Park J. LETM1 is required for mitochondrial homeostasis and cellular viability (Review). Mol Med Rep 2019; 19:3367-3375. [PMID: 30896806 PMCID: PMC6471456 DOI: 10.3892/mmr.2019.10041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
Leucine zipper/EF-hand-containing transmembrane protein 1 (LETM1) has been identified as the gene responsible for Wolf-Hirschhorn syndrome (WHS), which is characterized by intellectual disability, epilepsy, growth delay and craniofacial dysgenesis. LETM1 is a mitochondrial inner membrane protein that encodes a homolog of the yeast protein Mdm38, which is involved in mitochondrial morphology. In the present review, the importance of LETM1 in WHS and its role within the mitochondrion was explored. LETM1 governs the mitochondrion ion channel and is involved in mitochondrial respiration. Recent studies have reported that LETM1 acts as a mitochondrial Ca2+/H+ antiporter. LETM1 has also been identified as a K+/H+ exchanger, and serves a role in Mg2+ homeostasis. The function of LETM1 in mitochondria regulation is regulated by its binding partners, carboxyl-terminal modulator protein and mitochondrial ribosomal protein L36. Therefore, we describe the remarkable role of LETM1 in mitochondrial network physiology and its function in mitochondrion-mediated cell death. In the context of these findings, we suggest that the participation of LETM1 in tumorigenesis through the alteration of cancer metabolism should be investigated. This review provides a comprehensive description of LETM1 function, which is required for mitochondrial homeostasis and cellular viability.
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Affiliation(s)
- Yuwen Li
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Quangdon Tran
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Robin Shrestha
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Longzhen Piao
- Department of Oncology, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Sungjin Park
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jisoo Park
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Jongsun Park
- Department of Pharmacology, Metabolic Syndrome and Cell Signaling Laboratory, Institute for Cancer Research, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
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16
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ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells. Anal Cell Pathol (Amst) 2019; 2019:1575031. [PMID: 30881868 PMCID: PMC6387701 DOI: 10.1155/2019/1575031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/12/2018] [Accepted: 10/20/2018] [Indexed: 12/14/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB) is overexpressed and has an oncogenic role in hepatocellular carcinoma (HCC). Interleukin enhancer binding factor 2 (ILF2) has become research hotspot in liver cancer recently. However, it is still unclear whether and how CREB and ILF2 interact with each other. And how this interaction exerts its role in occurrence and development of liver cancer is still unclear. Here, we found that ILF2 directly bound with CREB, and this binding was essential for the malignant phenotypes of liver cancer cells. Moreover, we found that ILF2 acted as one of the upstream proteins of CREB and promoted CREB only in the protein level, whereas ILF2 expression was not regulated by CREB. Mechanistically, ILF2 bound to the pKID domain of CREB and stimulated its phosphorylation at Ser133. Taken together, our study finds a novel interaction between CREB and ILF2 in liver cancer, and this interaction might play a role in the diagnosis and remedy of liver cancer.
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17
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Expression and Critical Role of Interleukin Enhancer Binding Factor 2 in Hepatocellular Carcinoma. Int J Mol Sci 2016; 17:ijms17081373. [PMID: 27556459 PMCID: PMC5000768 DOI: 10.3390/ijms17081373] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 02/05/2023] Open
Abstract
Interleukin enhancer binding factor 2 (ILF2), a transcription factor, regulates cell growth by inhibiting the stabilization of mRNA. Currently, its role has gained recognition as a factor in the tumorigenic process. However, until now, little has been known about the detailed role ILF2 plays in hepatocellular carcinoma (HCC). In this study, we investigated the expression levels of ILF2 in HCC tissue with Western blot and immunohistochemical assays. To examine the effect of ILF2 on liver cancer cell growth and apoptosis, small interfering RNAs (siRNAs) targeting ILF2 were recombined to create lentiviral overexpression vectors. Our results showed higher expression levels of ILF2 mRNA and ILF2 protein in HCC tissue compared with matched peritumoral tissue. Expression of ILF2 may regulate cell growth and apoptosis in liver cancer cells via regulation of B-cell lymphoma 2 (Bcl-2), Bcl-2 related ovarian killer (Bok), Bcl-2-associated X protein (BAX), and cellular inhibitor of apoptosis 1 (cIAP1). Moreover, we inoculated nude mice with liver cancer cells to investigate the effect of ILF2 on tumorigenesis in vivo. As expected, a rapid growth was observed in cancer cells inoculated with a lentiviral vector coding Flag-ILF2 (Lenti-ILF2) compared with the control cells. Hence, these results promote a better understanding of ILF2’s potential role as a therapeutic target in HCC.
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18
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Xing X, Liang D, Huang Y, Zeng Y, Han X, Liu X, Liu J. The application of proteomics in different aspects of hepatocellular carcinoma research. J Proteomics 2016; 145:70-80. [DOI: 10.1016/j.jprot.2016.03.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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19
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Xing X, Huang Y, Wang S, Chi M, Zeng Y, Chen L, Li L, Zeng J, Lin M, Han X, Liu X, Liu J. Comparative analysis of primary hepatocellular carcinoma with single and multiple lesions by iTRAQ-based quantitative proteomics. J Proteomics 2015; 128:262-71. [DOI: 10.1016/j.jprot.2015.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 07/16/2015] [Accepted: 08/12/2015] [Indexed: 02/07/2023]
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20
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Ni T, Mao G, Xue Q, Liu Y, Chen B, Cui X, Lv L, Jia L, Wang Y, Ji L. Upregulated expression of ILF2 in non-small cell lung cancer is associated with tumor cell proliferation and poor prognosis. J Mol Histol 2015; 46:325-35. [DOI: 10.1007/s10735-015-9624-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/29/2015] [Indexed: 01/13/2023]
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21
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Wang CA, Liu Q, Chen Y, Liu S, Xu J, Cui X, Zhang Y, Piao L. Clinical implication of leucine zipper/EF hand-containing transmembrane-1 overexpression in the prognosis of triple-negative breast cancer. Exp Mol Pathol 2015; 98:254-9. [DOI: 10.1016/j.yexmp.2014.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 12/26/2014] [Indexed: 01/18/2023]
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22
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Vaitheesvaran B, Hartil K, Navare A, Zheng, ÓBroin P, Golden A, Guha, Lee WN, Kurland I, Bruce JE. Role of the tumor suppressor IQGAP2 in metabolic homeostasis: Possible link between diabetes and cancer. Metabolomics 2014; 10:920-937. [PMID: 25254002 PMCID: PMC4169985 DOI: 10.1007/s11306-014-0639-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Deficiency of IQGAP2, a scaffolding protein expressed primarily in liver leads to rearrangements of hepatic protein compartmentalization and altered regulation of enzyme functions predisposing development of hepatocellular carcinoma and diabetes. Employing a systems approach with proteomics, metabolomics and fluxes characterizations, we examined the effects of IQGAP2 deficient proteomic changes on cellular metabolism and the overall metabolic phenotype. Iqgap2-/- mice demonstrated metabolic inflexibility, fasting hyperglycemia and obesity. Such phenotypic characteristics were associated with aberrant hepatic regulations of glycolysis/gluconeogenesis, glycogenolysis, lipid homeostasis and futile cycling corroborated with corresponding proteomic changes in cytosolic and mitochondrial compartments. IQGAP2 deficiency also led to truncated TCA-cycle, increased anaplerosis, increased supply of acetyl-CoA for de novo lipogenesis, and increased mitochondrial methyl-donor metabolism necessary for nucleotides synthesis. Our results suggest that changes in metabolic networks in IQGAP2 deficiency create a hepatic environment of a 'pre-diabetic' phenotype and a predisposition to non-alcoholic fatty liver disease (NAFLD) which has been linked to the development of hepatocellular carcinoma.
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Affiliation(s)
- B. Vaitheesvaran
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - K. Hartil
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - A. Navare
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Zheng
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - P. ÓBroin
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
- Department of Genetics., Division of Computational Genetics, Albert Einstein College of Medicine, Bronx, NewYork, 10461
| | - A. Golden
- Department of Genetics., Division of Computational Genetics, Albert Einstein College of Medicine, Bronx, NewYork, 10461
| | - Guha
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - WN. Lee
- Department of Pediatrics, Division of Endocrinology and Metabolism, University of California, Los Angeles, California 90502
| | - I.J Kurland
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - J. E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
- Corresponding author: James E. Bruce. Department of Genome Sciences, University of Washington, Seattle, Washington, 98109., , Phone: 206-543-0220, Fax: 206-616-0008
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23
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Faye MD, Holcik M. The role of IRES trans-acting factors in carcinogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:887-97. [PMID: 25257759 DOI: 10.1016/j.bbagrm.2014.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/09/2014] [Accepted: 09/14/2014] [Indexed: 02/06/2023]
Abstract
Regulation of protein expression through RNA metabolism is a key aspect of cellular homeostasis. Upon specific cellular stresses, distinct transcripts are selectively controlled to modify protein output in order to quickly and appropriately respond to stress. Reprogramming of the translation machinery is one node of this strict control that typically consists of an attenuation of the global, cap-dependent translation and accompanying switch to alternative mechanisms of translation initiation, such as internal ribosome entry site (IRES)-mediated initiation. In cancer, many aspects of the RNA metabolism are frequently misregulated to provide cancer cells with a growth and survival advantage. This includes changes in the expression and function of RNA binding proteins termed IRES trans-acting factors (ITAFs) that are central to IRES translation. In this review, we will examine select emerging, as well as established, ITAFs with important roles in cancer initiation and progression, and in particular their role in IRES-mediated translation. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Mame Daro Faye
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada
| | - Martin Holcik
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada; Department of Pediatrics, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada.
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Lee JG, McKinney KQ, Mougeot JL, Bonkovsky HL, Hwang SI. Proteomic strategy for probing complementary lethality of kinase inhibitors against pancreatic cancer. Proteomics 2013; 13:3554-62. [DOI: 10.1002/pmic.201300248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/22/2013] [Accepted: 10/11/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Jin-Gyun Lee
- Proteomics and Mass Spectrometry Research Laboratory; Carolinas HealthCare System; Charlotte NC USA
| | - Kimberly Q. McKinney
- Proteomics and Mass Spectrometry Research Laboratory; Carolinas HealthCare System; Charlotte NC USA
| | - Jean-Luc Mougeot
- Department of Therapeutic Research and Development; Carolinas HealthCare System; Charlotte NC USA
| | - Herbert L. Bonkovsky
- Department of Therapeutic Research and Development; Carolinas HealthCare System; Charlotte NC USA
- Department of Medicine; Carolinas HealthCare System; Charlotte NC USA
| | - Sun-Il Hwang
- Proteomics and Mass Spectrometry Research Laboratory; Carolinas HealthCare System; Charlotte NC USA
- Department of Therapeutic Research and Development; Carolinas HealthCare System; Charlotte NC USA
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25
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Lee YY, Kim HP, Kang MJ, Cho BK, Han SW, Kim TY, Yi EC. Phosphoproteomic analysis identifies activated MET-axis PI3K/AKT and MAPK/ERK in lapatinib-resistant cancer cell line. Exp Mol Med 2013; 45:e64. [PMID: 24263233 PMCID: PMC3849569 DOI: 10.1038/emm.2013.115] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/25/2013] [Accepted: 08/06/2013] [Indexed: 12/22/2022] Open
Abstract
Lapatinib, a dual inhibitor of epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) tyrosine kinases, has shown promising results as a growth inhibitor of HER2-positive cancer cells in vitro. However, similar to other EGFR-targeting drugs, acquired resistance to lapatinib by HER2-positive cancer cells remains a major clinical challenge. To elucidate resistance mechanisms to EGFR/HER2-targeting agents, we performed a systematic quantitative comparison of the phosphoproteome of lapatinib-resistant (LR) human gastric cancer cells (SNU216-LR) versus parental cells (SNU216) using a titanium dioxide (TiO2) phosphopeptide enrichment method and analysis with a Q-Exactive hybrid quadrupole-Orbitrap mass spectrometer. Biological network analysis of differentially expressed phosphoproteins revealed apparent constitutive activation of the MET-axis phosphatidylinositide 3-kinase (PI3K)/α-serine/threonine-protein kinase (AKT) and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling pathways in SNU216-LR. Inhibition of the PI3K/AKT and MAPK/ERK signaling pathways in SNU216-LR also leads to cell cycle arrest, confirming the biological network analysis. Lapatinib sensitivity was restored when cells were treated with several molecular targeting agents in combination with lapatinib. Thus, by integrating phosphoproteomic data, protein networks and effects of signaling pathway modulation on cell proliferation, we found that SNU216-LR maintains constitutive activation of the PI3K/AKT and MAPK/ERK pathways in a MET-dependent manner. These findings suggest that pathway activation is a key compensatory intracellular phospho-signaling event that may govern gastric cancer cell resistance to drug treatment.
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Affiliation(s)
- Yong Yook Lee
- 1] WCU Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea [2] Wide River Institute of Immunology, Seoul National University, Seoul, Republic of Korea
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26
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Slany A, Haudek-Prinz V, Zwickl H, Stättner S, Grasl-Kraupp B, Gerner C. Myofibroblasts are important contributors to human hepatocellular carcinoma: Evidence for tumor promotion by proteome profiling. Electrophoresis 2013; 34:3315-25. [DOI: 10.1002/elps.201300326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/19/2013] [Accepted: 08/30/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Astrid Slany
- Faculty of Chemistry, Institute of Analytical Chemistry; University of Vienna; Austria
- Department of Medicine I; Comprehensive Cancer Center; Institute of Cancer Research; Medical University of Vienna; Austria
| | - Verena Haudek-Prinz
- Faculty of Chemistry, Institute of Analytical Chemistry; University of Vienna; Austria
- Department of Medicine I; Comprehensive Cancer Center; Institute of Cancer Research; Medical University of Vienna; Austria
| | - Hannes Zwickl
- Department of Medicine I; Comprehensive Cancer Center; Institute of Cancer Research; Medical University of Vienna; Austria
| | - Stefan Stättner
- Department of Surgery; Paracelsus Medical University; Salzburg Austria
| | - Bettina Grasl-Kraupp
- Department of Medicine I; Comprehensive Cancer Center; Institute of Cancer Research; Medical University of Vienna; Austria
| | - Christopher Gerner
- Faculty of Chemistry, Institute of Analytical Chemistry; University of Vienna; Austria
- Department of Medicine I; Comprehensive Cancer Center; Institute of Cancer Research; Medical University of Vienna; Austria
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Fye HKS, Wright-Drakesmith C, Kramer HB, Camey S, da Costa AN, Jeng A, Bah A, Kirk GD, Sharif MIF, Ladep NG, Okeke E, Hainaut P, Taylor-Robinson SD, Kessler BM, Mendy ME. Protein profiling in hepatocellular carcinoma by label-free quantitative proteomics in two west African populations. PLoS One 2013; 8:e68381. [PMID: 23935864 PMCID: PMC3728326 DOI: 10.1371/journal.pone.0068381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 05/28/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatocellular Carcinoma is the third most common cause of cancer related death worldwide, often diagnosed by measuring serum AFP; a poor performance stand-alone biomarker. With the aim of improving on this, our study focuses on plasma proteins identified by Mass Spectrometry in order to investigate and validate differences seen in the respective proteomes of controls and subjects with LC and HCC. METHODS Mass Spectrometry analysis using liquid chromatography electro spray ionization quadrupole time-of-flight was conducted on 339 subjects using a pooled expression profiling approach. ELISA assays were performed on four significantly differentially expressed proteins to validate their expression profiles in subjects from the Gambia and a pilot group from Nigeria. Results from this were collated for statistical multiplexing using logistic regression analysis. RESULTS Twenty-six proteins were identified as differentially expressed between the three subject groups. Direct measurements of four; hemopexin, alpha-1-antitrypsin, apolipoprotein A1 and complement component 3 confirmed their change in abundance in LC and HCC versus control patients. These trends were independently replicated in the pilot validation subjects from Nigeria. The statistical multiplexing of these proteins demonstrated performance comparable to or greater than ALT in identifying liver cirrhosis or carcinogenesis. This exercise also proposed preliminary cut offs with achievable sensitivity, specificity and AUC statistics greater than reported AFP averages. CONCLUSIONS The validated changes of expression in these proteins have the potential for development into high-performance tests usable in the diagnosis and or monitoring of HCC and LC patients. The identification of sustained expression trends strengthens the suggestion of these four proteins as worthy candidates for further investigation in the context of liver disease. The statistical combinations also provide a novel inroad of analyses able to propose definitive cut-offs and combinations for evaluation of performance.
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Affiliation(s)
- Haddy K. S. Fye
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Cynthia Wright-Drakesmith
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Holger B. Kramer
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Suzi Camey
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- Departamento de Estatistica, Instituto de Matematica, Universidade Federal do Rio Grande do Sul, Rio Grande, Brazil
| | - Andre Nogueira da Costa
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
| | - Adam Jeng
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Alasana Bah
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Gregory D. Kirk
- Department of Epidemiology - Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Mohamed I. F. Sharif
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Nimzing G. Ladep
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Edith Okeke
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Pierre Hainaut
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- The International Prevention Research Institute, Lyon, France
| | - Simon D. Taylor-Robinson
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Maimuna E. Mendy
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
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28
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Goh WWB, Sergot MJ, Sng JCG, Sng JC, Wong L. Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice. J Proteome Res 2013; 12:2116-27. [PMID: 23557376 PMCID: PMC3805323 DOI: 10.1021/pr301127f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Despite
its prominence for characterization of complex mixtures,
LC–MS/MS frequently fails to identify many proteins. Network-based
analysis methods, based on protein–protein interaction networks
(PPINs), biological pathways, and protein complexes, are useful for
recovering non-detected proteins, thereby enhancing analytical resolution.
However, network-based analysis methods do come in varied flavors
for which the respective efficacies are largely unknown. We compare
the recovery performance and functional insights from three distinct
instances of PPIN-based approaches, viz., Proteomics Expansion Pipeline
(PEP), Functional Class Scoring (FCS), and Maxlink, in a test scenario
of valproic acid (VPA)-treated mice. We find that the most comprehensive
functional insights, as well as best non-detected protein recovery
performance, are derived from FCS utilizing real biological complexes.
This outstrips other network-based methods such as Maxlink or Proteomics
Expansion Pipeline (PEP). From FCS, we identified known biological
complexes involved in epigenetic modifications, neuronal system development,
and cytoskeletal rearrangements. This is congruent with the observed
phenotype where adult mice showed an increase in dendritic branching
to allow the rewiring of visual cortical circuitry and an improvement
in their visual acuity when tested behaviorally. In addition, PEP
also identified a novel complex, comprising YWHAB, NR1, NR2B, ACTB,
and TJP1, which is functionally related to the observed phenotype.
Although our results suggest different network analysis methods can
produce different results, on the whole, the findings are mutually
supportive. More critically, the non-overlapping information each
provides can provide greater holistic understanding of complex phenotypes.
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Goh WWB, Wong L. Networks in proteomics analysis of cancer. Curr Opin Biotechnol 2013; 24:1122-8. [PMID: 23481377 DOI: 10.1016/j.copbio.2013.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/07/2013] [Accepted: 02/09/2013] [Indexed: 01/08/2023]
Abstract
Proteomics provides direct biological information on proteins but is still a limited platform. Borrowing from genomics, its cancer-specific applications can be broadly categorized as (1) pure diagnostics, (2) biomarkers, (3) identification of root causes and (4) identification of cancer-specific network rewirings. Biological networks capture complex relationships between proteins and provide an appropriate means of contextualization. While playing significantly larger roles, especially in 1 and 3, progress in proteomics-specific network-based methods is lagging as compared to genomics. Rapid hardware advances and improvements in proteomic identification and quantification have given rise to much better quality data alongside advent of new network-based analysis methods. However, a tighter integration between analytics and hardware is still essential for network analysis to play more significant roles in proteomics analysis.
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Affiliation(s)
- Wilson Wen Bin Goh
- Department of Computer Science, National University of Singapore, COM1 Building, 13 Computing Drive, Singapore 117417, Singapore; Department of Computing, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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D'Alessandro LA, Meyer R, Klingmüller U. Hepatocellular carcinoma: a systems biology perspective. Front Physiol 2013; 4:28. [PMID: 23444340 PMCID: PMC3580827 DOI: 10.3389/fphys.2013.00028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/06/2013] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinomas (HCCs) have different etiology and heterogenic genomic alterations lead to high complexity. The molecular features of HCC have largely been studied by gene expression and proteome profiling focusing on the correlations between the expression of specific markers and clinical data. Integration of the increasing amounts of data in databases has facilitated the link of genomic and proteomic profiles of HCC to disease state and clinical outcome. Despite the current knowledge, specific molecular markers remain to be identified and new strategies are required to establish novel-targeted therapies. In the last years, mathematical models reconstructing gene and protein networks based on experimental data of HCC have been developed providing powerful tools to predict candidate interactions and potential targets for therapy. Furthermore, the combination of dynamic and logical mathematical models with quantitative data allows detailed mechanistic insights into system properties. To address effects at the organ level, mathematical models reconstructing the three-dimensional organization of liver lobules were developed. In the future, integration of different modeling approaches capturing the effects at the cellular up to the organ level is required to address the complex properties of HCC and to enable the discovery of new targets for HCC prevention or treatment.
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Affiliation(s)
- Lorenza A D'Alessandro
- Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Centre (DKFZ) Heidelberg, Germany
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Hwang SI, Han DK. Subcellular fractionation for identification of biomarkers: serial detergent extraction by subcellular accessibility and solubility. Methods Mol Biol 2013; 1002:25-35. [PMID: 23625392 DOI: 10.1007/978-1-62703-360-2_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cellular localization of proteins is one of the most valuable sources of information regarding spatiotemporal biological events involved in human disease. This information is sometimes enhanced by carrying out protein isolation using a process known as subcellular fractionation. This involves the sequential extraction of proteins from specific compartments and/or organelles within the cell. Additionally, subcellular fractionation for biomarker discovery enables the in-depth analysis of biomolecules by reducing the complexity of the protein mixture. In this chapter, four custom fractionation approaches and one commercial kit are compared for their efficacy and compatibility with subsequent proteomic analysis.
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Watch the GAP: Emerging Roles for IQ Motif-Containing GTPase-Activating Proteins IQGAPs in Hepatocellular Carcinoma. Int J Hepatol 2012; 2012:958673. [PMID: 22973521 PMCID: PMC3438877 DOI: 10.1155/2012/958673] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/25/2012] [Accepted: 08/03/2012] [Indexed: 12/12/2022] Open
Abstract
IQ motif-containing GTPase-activating proteins IQGAP1 and IQGAP2 are highly homologous multidomain scaffolding proteins. Their major function consists of integration of Rho GTPase and Ca(2+)/calmodulin signals with cell adhesive and cytoskeletal reorganizational events. Recent studies showed that they play an important role in carcinogenesis. There is growing evidence that IQGAP2 is a novel tumor suppressor counteracting the effects of IQGAP1, an oncogene, in several cancers, especially in hepatocellular carcinoma (HCC). While HCC is highly prevalent and one of the deadliest cancers worldwide, the signaling pathways involved are not fully understood and treatment of advanced disease still represents an area of high unmet medical need. This paper compiles various findings from studies in mouse models, cell lines, and patient samples that support future development of IQGAPs into new therapeutic targets. It also discusses distinct features of IQGAP2 in an attempt to provide insight into the mechanism of the seemingly paradoxical opposing roles of the two very similar IQGAP proteins in carcinogenesis.
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