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Reddi KK, Zhang W, Shahrabi-Farahani S, Anderson KM, Liu M, Kakhniashvili D, Wang X, Zhang YH. Tetraspanin CD82 Correlates with and May Regulate S100A7 Expression in Oral Cancer. Int J Mol Sci 2024; 25:2659. [PMID: 38473906 PMCID: PMC10932236 DOI: 10.3390/ijms25052659] [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: 01/21/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Many metastatic cancers with poor prognoses correlate to downregulated CD82, but exceptions exist. Understanding the context of this correlation is essential to CD82 as a prognostic biomarker and therapeutic target. Oral squamous cell carcinoma (OSCC) constitutes over 90% of oral cancer. We aimed to uncover the function and mechanism of CD82 in OSCC. We investigated CD82 in human OSCC cell lines, tissues, and healthy controls using the CRISPR-Cas9 gene knockout, transcriptomics, proteomics, etc. CD82 expression is elevated in CAL 27 cells. Knockout CD82 altered over 300 genes and proteins and inhibited cell migration. Furthermore, CD82 expression correlates with S100 proteins in CAL 27, CD82KO, SCC-25, and S-G cells and some OSCC tissues. The 37-50 kDa CD82 protein in CAL 27 cells is upregulated, glycosylated, and truncated. CD82 correlates with S100 proteins and may regulate their expression and cell migration. The truncated CD82 explains the invasive metastasis and poor outcome of the CAL 27 donor. OSCC with upregulated truncated CD82 and S100A7 may represent a distinct subtype with a poor prognosis. Differing alternatives from wild-type CD82 may elucidate the contradictory functions and pave the way for CD82 as a prognostic biomarker and therapeutic target.
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Affiliation(s)
- Kiran Kumar Reddi
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, 875 Union Ave, Memphis, TN 38163, USA
| | - Weiqiang Zhang
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- USDA-ARS, Pollinator Health in Southern Crop Ecosystem Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
| | - Shokoufeh Shahrabi-Farahani
- Department of Diagnostic Sciences, College of Dentistry, University of Tennessee Health Science Center, 875 Union Ave, Memphis, TN 38163, USA
| | - Kenneth Mark Anderson
- Department of Diagnostic Sciences, College of Dentistry, University of Tennessee Health Science Center, 875 Union Ave, Memphis, TN 38163, USA
| | - Mingyue Liu
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, 875 Union Ave, Memphis, TN 38163, USA
| | - David Kakhniashvili
- The Proteomics & Metabolomics Core Facility, University of Tennessee Health Science Center, 71 S. Manassas, Suite 110, Memphis, TN 38163, USA
| | - Xusheng Wang
- Department of Genetics, Genomics & Informatics, University of Tennessee Health Science Center, 71 S. Manassas, Room 410H, Memphis, TN 38163, USA
| | - Yanhui H. Zhang
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, 875 Union Ave, Memphis, TN 38163, USA
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Glathar AR, Oyelakin A, Nayak KB, Sosa J, Romano RA, Sinha S. A Systemic and Integrated Analysis of p63-Driven Regulatory Networks in Mouse Oral Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:446. [PMID: 36672394 PMCID: PMC9856320 DOI: 10.3390/cancers15020446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of disease etiology, and delayed diagnoses continue to negatively affect survival. The identification of oncogenic drivers and prognostic biomarkers by leveraging bulk and single-cell RNA-sequencing datasets of OSCC can lead to more targeted therapies and improved patient outcomes. However, the generation, analysis, and continued utilization of additional genetic and genomic tools are warranted. Tobacco-induced OSCC can be modeled in mice via 4-nitroquinoline 1-oxide (4NQO), which generates a spectrum of neoplastic lesions mimicking human OSCC and upregulates the oncogenic master transcription factor p63. Here, we molecularly characterized established mouse 4NQO treatment-derived OSCC cell lines and utilized RNA and chromatin immunoprecipitation-sequencing to uncover the global p63 gene regulatory and signaling network. We integrated our p63 datasets with published bulk and single-cell RNA-sequencing of mouse 4NQO-treated tongue and esophageal tumors, respectively, to generate a p63-driven gene signature that sheds new light on the role of p63 in murine OSCC. Our analyses reveal known and novel players, such as COTL1, that are regulated by p63 and influence various oncogenic processes, including metastasis. The identification of new sets of potential biomarkers and pathways, some of which are functionally conserved in human OSCC and can prognosticate patient survival, offers new avenues for future mechanistic studies.
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Affiliation(s)
- Alexandra Ruth Glathar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Akinsola Oyelakin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Kasturi Bala Nayak
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jennifer Sosa
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Rose-Anne Romano
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
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3
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RAGE Inhibitors for Targeted Therapy of Cancer: A Comprehensive Review. Int J Mol Sci 2022; 24:ijms24010266. [PMID: 36613714 PMCID: PMC9820344 DOI: 10.3390/ijms24010266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
The receptor for advanced glycation end products (RAGE) is a member of the immunoglobulin family that is overexpressed in several cancers. RAGE is highly expressed in the lung, and its expression increases proportionally at the site of inflammation. This receptor can bind a variety of ligands, including advanced glycation end products, high mobility group box 1, S100 proteins, adhesion molecules, complement components, advanced lipoxidation end products, lipopolysaccharides, and other molecules that mediate cellular responses related to acute and chronic inflammation. RAGE serves as an important node for the initiation and stimulation of cell stress and growth signaling mechanisms that promote carcinogenesis, tumor propagation, and metastatic potential. In this review, we discuss different aspects of RAGE and its prominent ligands implicated in cancer pathogenesis and describe current findings that provide insights into the significant role played by RAGE in cancer. Cancer development can be hindered by inhibiting the interaction of RAGE with its ligands, and this could provide an effective strategy for cancer treatment.
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4
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Evaluation of Heterogeneous Nuclear Ribonucleoprotein D Expression as a Diagnostic Marker for Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2022; 12:diagnostics12061332. [PMID: 35741145 PMCID: PMC9221583 DOI: 10.3390/diagnostics12061332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein D (hnRNPD) serves as a prognostic marker for oral squamous cell carcinoma (OSCC). We evaluated the diagnostic potential of hnRNPD to differentiate between OSCC and normal mucosa. Immunohistochemistry for hnRNPD and a routinely used diagnostic marker deltaNp63 (p40) was performed in 32 normal mucosae and 46 OSCC specimens. Subsequently, receiver-operating characteristic analysis was performed to evaluate the diagnostic potential of hnRNPD in comparison to that of p40. Immunostaining for p40 and hnRNPD was observed in 39 (84.78%) and 38 (82.60%) cases, respectively, in OSCC specimens. The poorly differentiated squamous cell carcinoma displayed 100% (eight cases) immunoreactivity for hnRNPD as compared to 87.5% (seven cases) for p40. Nuclear staining of p40 and hnRNPD was observed in all OSCC specimens. p40 staining was restricted to basal cells, whereas both basal and para-basal cells displayed hnRNPD staining in OSCC specimens. Areas under the curve for p40 and hnRNPD were 0.86 and 0.87, respectively. p40 and hnRNPD showed equal sensitivities (80.95%). However, hnRNPD displayed marginally higher (88.23%) specificity for tumor cells as compared to that of p40 (85.29%). Conclusion: In addition to being a well-established prognostic marker, hnRNPD can serve as a diagnostic marker for OSCC.
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Pinto VB, Almeida VC, Pereira-Lima ÍA, Vale EM, Araújo WL, Silveira V, Viana JMS. Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics. PLANTA 2021; 254:132. [PMID: 34821986 DOI: 10.1007/s00425-021-03786-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Al responsive proteins are associated with starch, sucrose, and other carbohydrate metabolic pathways. Sucrose synthase is a candidate to Al tolerance. Al responses are regulated at transcriptional and post-transcriptional levels. Aluminum toxicity is one of the important abiotic stresses that affects worldwide crop production. The soluble form of aluminum (Al3+) inhibits root growth by altering water and nutrient uptake, a process that also reduces plant growth and development. Under long-term Al3+ exposure, plants can activate several tolerance mechanisms. To date, no reports of large-scale proteomic data concerning maize responses to this ion have been published. To investigate the post-transcriptional regulation in response to Al toxicity, we performed label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress conditions. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch, sucrose, and other components of carbohydrate metabolism and glycolysis/gluconeogenesis are the biochemical processes regulated in response to Al toxicity. Sucrose synthase accumulation and an increase in sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The accumulation of citrate synthase suggests a key role for this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicates that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn root development.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil.
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil.
| | - Vinicius Costa Almeida
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ítalo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
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Pillai J, Chincholkar T, Dixit R, Pandey M. A systematic review of proteomic biomarkers in oral squamous cell cancer. World J Surg Oncol 2021; 19:315. [PMID: 34711249 PMCID: PMC8555221 DOI: 10.1186/s12957-021-02423-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Head and neck squamous cell cancer (HNSCC) is the most common cancer associated with chewing tobacco, in the world. As this is divided in to sites and subsites, it does not make it to top 10 cancers. The most common subsite is the oral cancer. At the time of diagnosis, more than 50% of patients with oral squamous cell cancers (OSCC) had advanced disease, indicating the lack of availability of early detection and risk assessment biomarkers. The new protein biomarker development and discovery will aid in early diagnosis and treatment which lead to targeted treatment and ultimately a good prognosis. METHODS This systematic review was performed as per PRISMA guidelines. All relevant studies assessing characteristics of oral cancer and proteomics were considered for analysis. Only human studies published in English were included, and abstracts, incomplete articles, and cell line or animal studies were excluded. RESULTS A total of 308 articles were found, of which 112 were found to be relevant after exclusion. The present review focuses on techniques of cancer proteomics and discovery of biomarkers using these techniques. The signature of protein expression may be used to predict drug response and clinical course of disease and could be used to individualize therapy with such knowledge. CONCLUSIONS Prospective use of these markers in the clinical setting will enable early detection, prediction of response to treatment, improvement in treatment selection, and early detection of tumor recurrence for disease monitoring. However, most of these markers for OSCC are yet to be validated.
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Affiliation(s)
| | | | - Ruhi Dixit
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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7
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Chang LC, Hsu YC, Chiu HM, Ueda K, Wu MS, Kao CH, Shen TL. Exploration of the Proteomic Landscape of Small Extracellular Vesicles in Serum as Biomarkers for Early Detection of Colorectal Neoplasia. Front Oncol 2021; 11:732743. [PMID: 34589434 PMCID: PMC8473825 DOI: 10.3389/fonc.2021.732743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background Patient participation in colorectal cancer (CRC) screening via a stool test and colonoscopy is suboptimal, but participation can be improved by the development of a blood test. However, the suboptimal detection abilities of blood tests for advanced neoplasia, including advanced adenoma (AA) and CRC, limit their application. We aimed to investigate the proteomic landscape of small extracellular vesicles (sEVs) from the serum of patients with colorectal neoplasia and identify specific sEV proteins that could serve as biomarkers for early diagnosis. Materials and Methods We enrolled 100 patients including 13 healthy subjects, 12 non-AAs, 13 AAs, and 16 stage-I, 15 stage-II, 16 stage-III, and 15 stage-IV CRCs. These patients were classified as normal control, early neoplasia, and advanced neoplasia. The sEV proteome was explored by liquid chromatography-tandem mass spectrometry. Generalized association plots were used to integrate the clustering methods, visualize the data matrix, and analyze the relationship. The specific sEV biomarkers were identified by a decision tree via Orange3 software. Functional enrichment analysis was conducted by using the Ingenuity Pathway Analysis platform. Results The sEV protein matrix was identified from the serum of 100 patients and contained 3353 proteins, of which 1921 proteins from 98 patients were finally analyzed. Compared with the normal control, subjects with early and advanced neoplasia exhibited a distinct proteomic distribution in the data matrix plot. Six sEV proteins were identified, namely, GCLM, KEL, APOF, CFB, PDE5A, and ATIC, which properly distinguished normal control, early neoplasia, and advanced neoplasia patients from each other. Functional enrichment analysis revealed that APOF+ and CFB+ sEV associated with clathrin-mediated endocytosis signaling and the complement system, which have critical implications for CRC carcinogenesis. Conclusion Patients with colorectal neoplasia had a distinct sEV proteome expression pattern in serum compared with those patients who were healthy and did not have neoplasms. Moreover, the six identified specific sEV proteins had the potential to discriminate colorectal neoplasia between early-stage and advanced neoplasia. Collectively, our study provided a six-sEV protein biomarker panel for CRC diagnosis at early or advanced stages. Furthermore, the implication of the sEV proteome in CRC carcinogenesis via specific signaling pathways was explored.
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Affiliation(s)
- Li-Chun Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Health Management Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Chiung Hsu
- Department of Biomedical Science and Engineering, National Central University, Taoyuan, Taiwan
| | - Han-Mo Chiu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Health Management Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Koji Ueda
- Cancer Precision Medicine Center, Japanese Foundation of Cancer Research, Tokyo, Japan
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-How Kao
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Tang-Long Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
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8
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Detection of Circulating Serum Protein Biomarkers of Non-Muscle Invasive Bladder Cancer after Protein Corona-Silver Nanoparticles Analysis by SWATH-MS. NANOMATERIALS 2021; 11:nano11092384. [PMID: 34578700 PMCID: PMC8467878 DOI: 10.3390/nano11092384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022]
Abstract
Because cystoscopy is expensive and invasive, a new method of detecting non-invasive muscular bladder cancer (NMIBC) is needed. This study aims to identify potential serum protein markers for NMIBC to improve diagnosis and to find treatment approaches that avoid disease progression to a life-threatening phenotype (muscle-invasive bladder cancer, MIBC). Here, silver nanoparticles (AgNPs, 9.73 ± 1.70 nm) as a scavenging device together with sequential window acquisition of all theoretical mass spectra (SWATH-MS) were used to quantitatively analyze the blood serum protein alterations in two NMIBC subtypes, T1 and Ta, and they were compared to normal samples (HC). NMIBC’s analysis of serum samples identified three major groups of proteins, the relative content of which is different from the HC content: proteins implicated in the complement and coagulation cascade pathways and apolipoproteins. In conclusion, many biomarker proteins were identified that merit further examination to validate their useful significance and utility within the clinical management of NMIBC patients.
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9
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Kim JA, Vetrivel P, Kim SM, Ha SE, Kim HH, Bhosale PB, Heo JD, Lee WS, Senthil K, Kim GS. Quantitative Proteomics Analysis for the Identification of Differential Protein Expression in Calf Muscles between Young and Old SD Rats Using Mass Spectrometry. ACS OMEGA 2021; 6:7422-7433. [PMID: 33778255 PMCID: PMC7992086 DOI: 10.1021/acsomega.0c05821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 05/04/2023]
Abstract
Aging is associated with loss of muscle mass and strength that leads to a condition termed sarcopenia. Impaired conditions, morbidity, and malnutrition are the factors of devaluation of muscle fibers in aged animals. Satellite cells play an important role in maintaining muscle homeostasis during tissue regeneration and repair. Proteomic profiling on the skeletal muscle tissues of different age group rats helps to determine the differentially expressed (DE) proteins, which may eventually lead to the development of biomarkers in treating the conditions of sarcopenia. In this study, nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis was implemented in the calf tissues of young and old groups of rats. The mass spectrometry (MS) analysis revealed the presence of 335 differentially expressed proteins between the two different age conditions, among which those based on log-fold change 25 proteins were upregulated and 77 were downregulated. The protein-protein interaction network analysis revealed 18 upregulated proteins with three distinct interconnected networks and 57 downregulated proteins with two networks. Further, gene ontology (GO) enrichment analysis showed the biological process, cellular component, and molecular function of the differential proteins. Pathway enrichment analysis of the DE proteins identified nine significantly enriched pathways with a list of eight significant genes (Cryab, Hspb2, Acat1, Ak1, Adssl1, Anxa5, Gys1, Ogdh, Gc, and Adssl1). Quantification of significant genes by quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the downregulation at the mRNA level. Western blot analysis of their protein expression showed concordant results on two candidate proteins (Ogdh and annexin 5) confirming their differential regulation between the two age groups of rats. Thus, these proteomic approaches on young and aged rats provide insights into the development of protein targets in the treatment of sarcopenia (muscle loss).
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Affiliation(s)
- Jin A. Kim
- Department
of Physical Therapy, International University
of Korea, Jinju 52833, Republic of Korea
| | - Preethi Vetrivel
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Seong Min Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Sang Eun Ha
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Hun Hwan Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Jeong Doo Heo
- Gyeongnam
Department of Environment Toxicology and Chemistry, Toxicity Screening
Research Center, Korea Institute of Toxicology, Munsan-eup, Jinju, Gyeongnam 52834, Republic of Korea
| | - Won Sup Lee
- Department
of Internal Medicine, Institute of Health Sciences, Gyeongsang National
University Hospital, Gyeongsang National
University School of Medicine, Jinju 660-702, Republic
of Korea
| | - Kalaiselvi Senthil
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, India
| | - Gon Sup Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
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Xu HY, Song HM, Zhou Q. Comprehensive analysis of the expression and prognosis for S100 in human ovarian cancer: A STROBE study. Medicine (Baltimore) 2020; 99:e22777. [PMID: 33217795 PMCID: PMC7676574 DOI: 10.1097/md.0000000000022777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
S100 family members are frequently deregulated in human malignancies, including ovarian cancer. However, the prognostic roles of each individual S100 family member in ovarian cancer (OC) patients remain elusive. In the present study, we assessed the prognostic roles and molecular function of 20 individual members of the S100 family in OC patients using GEPIA, Kaplan-Meier plotter, SurvExpress, GeneMANIA and Funrich database. Our results indicated that the mRNA expression levels of S100A1, S100A2, S100A4, S100A5, S100A11, S100A14, and S100A16 were significantly upregulated in patients with OC, and high mRNA expression of S100A1, S100A3, S100A5, S100A6, and S100A13 were significantly correlated with better overall survival, while increased S100A2, S100A7A, S100A10, and S100A11 mRNA expressions were associated with worse prognosis in OC patients. In stratified analysis, the trends of high expression of individual S100 members were nearly the same in different pathological grade, clinical stage, TP53 mutation status, and treatment. More importantly, S100 family signatures may be useful potential prognostic markers for OC. These findings suggest that S100 family plays a vital role in prognostic value and could potentially be an S100-targeted inhibitors for OC patients.
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Affiliation(s)
- Hong-Yu Xu
- Department of Gynecology and Obstetrics, the Second People's Hospital of Yichang, China Three Gorges University
| | - Hua-Mei Song
- Department of Gynecology and Obstetrics, the People's Hospital of China Three Gorges University/the First People's Hospital of Yichang, Yichang, Hubei, China
| | - Quan Zhou
- Department of Gynecology and Obstetrics, the People's Hospital of China Three Gorges University/the First People's Hospital of Yichang, Yichang, Hubei, China
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11
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [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: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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12
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Li CY, Cai JH, Tsai JJP, Wang CCN. Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis. Front Oncol 2020; 10:681. [PMID: 32528874 PMCID: PMC7258718 DOI: 10.3389/fonc.2020.00681] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/09/2020] [Indexed: 12/27/2022] Open
Abstract
Improved insight into the molecular mechanisms of head and neck squamous cell carcinoma (HNSCC) is required to predict prognosis and develop a new therapeutic strategy for targeted genes. The aim of this study is to identify significant genes associated with HNSCC and to further analyze its prognostic significance. In our study, the cancer genome atlas (TCGA) HNSCC database and the gene expression profiles of GSE6631 from the Gene Expression Omnibus (GEO) were used to explore the differential co-expression genes in HNSCC compared with normal tissues. A total of 29 differential co-expression genes were screened out by Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis methods. As suggested in functional annotation analysis using the R clusterProfiler package, these genes were mainly enriched in epidermis development and differentiation (biological process), apical plasma membrane and cell-cell junction (cellular component), and enzyme inhibitor activity (molecular function). Furthermore, in a protein-protein interaction (PPI) network containing 21 nodes and 25 edges, the ten hub genes (S100A8, S100A9, IL1RN, CSTA, ANXA1, KRT4, TGM3, SCEL, PPL, and PSCA) were identified using the CytoHubba plugin of Cytoscape. The expression of the ten hub genes were all downregulated in HNSCC tissues compared with normal tissues. Based on survival analysis, the lower expression of CSTA was associated with worse overall survival (OS) in patients with HNSCC. Finally, the protein level of CSTA, which was validated by the Human Protein Atlas (HPA) database, was down-regulated consistently with mRNA levels in head and neck cancer samples. In summary, our study demonstrated that a survival-related gene is highly correlated with head and neck cancer development. Thus, CSTA may play important roles in the progression of head and neck cancer and serve as a potential biomarker for future diagnosis and treatment.
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Affiliation(s)
- Chia Ying Li
- Department of Surgery, Show Chwan Memorial Hospital, Changhua, Taiwan.,Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jia-Hua Cai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Jeffrey J P Tsai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Charles C N Wang
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
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13
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Komaromy A, Reider B, Jarvas G, Guttman A. Glycoprotein biomarkers and analysis in chronic obstructive pulmonary disease and lung cancer with special focus on serum immunoglobulin G. Clin Chim Acta 2020; 506:204-213. [PMID: 32243984 DOI: 10.1016/j.cca.2020.03.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 01/11/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and lung cancer are two major diseases of the lung with high rate of mortality, mostly among tobacco smokers. The glycosylation patterns of various plasma proteins show significant changes in COPD and subsequent hypoxia, inflammation and lung cancer, providing promising opportunities for screening aberrant glycan structures contribute to early detection of both diseases. Glycoproteins associated with COPD and lung cancer consist of highly sialylated N-glycans, which play an important role in inflammation whereby hypoxia leads to accumulation of sialyl Lewis A and X glycans. Although COPD is an inflammatory disease, it is an independent risk factor for lung cancer. Marked decrease in galactosylation of plasma immunoglobulin G (IgG) together with increased presence of sialic acids and more complex highly branched N-glycan structures are characteristic for COPD and lung cancer. Numerous glycan biomarkers have been discovered, and analysis of glycovariants associated with COPD and lung cancer has been carried out. In this paper we review fundamental glycosylation changes in COPD and lung cancer glycoproteins, focusing on IgG to provide an opportunity to distinguish between the two diseases at the glycoprotein level with diagnostic value.
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Affiliation(s)
- Andras Komaromy
- University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary
| | - Balazs Reider
- University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary
| | - Gabor Jarvas
- University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Krt, Debrecen 4032, Hungary.
| | - Andras Guttman
- University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Krt, Debrecen 4032, Hungary
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14
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Li Y, Yang B, Tian J, Sun W, Wang G, Qian A, Wang C, Shan X, Kang Y. An iTRAQ-Based Comparative Proteomics Analysis of the Biofilm and Planktonic States of Aeromonas veronii TH0426. Int J Mol Sci 2020; 21:ijms21041450. [PMID: 32093365 PMCID: PMC7073075 DOI: 10.3390/ijms21041450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
Aeromonas veronii is a virulent fish pathogen that causes extensive economic losses in the aquaculture industry worldwide. In this study, a virulent strain of A. veronii TH0426 was used to establish an in vitro biofilm model. The results show that the biofilm-forming abilities of A. veronii TH0426 were similar in different media, peaking under conditions of 20 °C and pH 6. Further, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods were used to compare the differential expression of A. veronii between the biofilm and planktonic cells. The results show alterations in 277 proteins, with 130 being upregulated and 147 downregulated. Pathway analysis and GO (Gene Ontology) annotations indicated that these proteins are mainly involved in metabolic pathways and the biosynthesis of secondary metabolites and antibiotics. These proteins are the main factors affecting the adaptability of A. veronii to its external environment. MRM (multiple reaction 27 monitoring) and qPCR (qPCR) were used to verify the differential proteins of the selected A. veronii. This is the first report on the biofilm and planktonic cells of A. veronii, thus contributing to studying the infection and pathogenesis of A. veronii.
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Affiliation(s)
- Ying Li
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Bintong Yang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- College of Life Science, Changchun Sci-Tech University, Changchun 130118, China
| | - Jiaxin Tian
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Wuwen Sun
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Guiqin Wang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Aidong Qian
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Chunfeng Wang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
| | - Xiaofeng Shan
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- Correspondence: (X.-F.S.); (Y.-H.K.); Tel.: +86-13504404077 (X.S.); +86-0431-84533426 (Y.K.)
| | - Yuanhuan Kang
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (B.Y.); (J.T.); (W.S.); (G.W.); (A.Q.); (C.W.)
- Correspondence: (X.-F.S.); (Y.-H.K.); Tel.: +86-13504404077 (X.S.); +86-0431-84533426 (Y.K.)
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15
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Baslam M, Kaneko K, Mitsui T. iTRAQ-Based Proteomic Analysis of Rice Grains. Methods Mol Biol 2020; 2139:405-414. [PMID: 32462602 DOI: 10.1007/978-1-0716-0528-8_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cereal proteins have formed the basis of human diet worldwide, and their level of consumption is expected to increase. The knowledge of the protein composition and variation of the cereal grains is helpful for characterizing cereal varieties and to identify biomarkers for tolerance mechanisms. Grains produce a wide array of proteins, differing under conditions. Quantitative proteomics is a powerful approach allowing the identification of proteins expressed under defined conditions that may contribute understanding the complex biological systems of grains. Isobaric tags for relative and absolute quantitation (iTRAQ) is a mass spectrometry-based quantitative approach allowing, simultaneously, for protein identification and quantification from multiple samples with high coverage. One of the challenges in identifying grains proteins is their relatively high content (~90-95%) of carbohydrate (starch) and low protein (~4-10%) and lipid (~1%) fractions. In this chapter, we present a robust workflow to carry out iTRAQ quantification of the starchy rice grains.
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Affiliation(s)
- Marouane Baslam
- Department of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Toshiaki Mitsui
- Department of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan. .,Graduate School of Science and Technology, Niigata University, Niigata, Japan.
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16
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Seo SB, Baek JY, Lim JH, Jin X, Lee MY, Lee JH. 14-3-3ζ targeting induced senescence in Hep-2 laryngeal cancer cell through deneddylation of Cullin1 in the Skp1-Cullin-F-box protein complex. Cell Prolif 2019; 52:e12654. [PMID: 31222857 PMCID: PMC6797561 DOI: 10.1111/cpr.12654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Objectives Despite of the aberrant expression of 14‐3‐3ζ in head and neck squamous cell carcinoma (HNSCC), little is known about the role of 14‐3‐3ζ in the regulation of senescence in HNSCC. This study was performed to investigate whether 14‐3‐3ζ is implicated in senescence evasion of Hep‐2 laryngeal cancer cells. Methods The expression of 14‐3‐3ζ was suppressed using RNA interference strategy. Senescence induction was determined by senescence‐associated β‐galactosidase staining and the numbers of promyelocytic leukaemia nuclear body. Real‐time PCR, western blotting and immunohistochemistry were applied for the expression of corresponding proteins. Xenograft experiment was performed to show in vivo effect of 14‐3‐3ζ silencing on tumour growth. Results 14‐3‐3ζ silencing significantly induced senescence phenotypes via 27 accumulations. Subsequently, we demonstrated that p27 accumulation is linked to inactivation of SCFSkp2 complex activity, probably due to the deneddylation of cullin‐1 (Cul‐1) as follows. (a) Neddylated Cul‐1 is decreased by 14‐3‐3ζ silencing. (b) Blocking neddylation using MLN4924 reproduces senescence phenotypes. (c) Knockdown of CSN5, which functions as a deneddylase, was shown to restore the senescence phenotypes induced by 14‐3‐3ζ depletion. Finally, we demonstrated that 14‐3‐3ζ depletion effectively hindered the proliferation of Hep‐2 cells implanted into nude mice. Conclusion 14‐3‐3ζ negatively regulates senescence in Hep‐2 cells, suggesting that 14‐3‐3ζ targeting may serve to suppress the expansion of laryngeal cancer via induction of senescence through the Cul‐1/SCFSkp2/p27 axis.
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Affiliation(s)
- Sung Bin Seo
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ji-Ye Baek
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ji-Hee Lim
- Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Division of Nephrology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Xuyan Jin
- Department of Biomedicine and Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Anatomy, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Mun-Yong Lee
- Department of Anatomy, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, Graduate School, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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17
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Narasimhan M, Kannan S, Chawade A, Bhattacharjee A, Govekar R. Clinical biomarker discovery by SWATH-MS based label-free quantitative proteomics: impact of criteria for identification of differentiators and data normalization method. J Transl Med 2019; 17:184. [PMID: 31151397 PMCID: PMC6545036 DOI: 10.1186/s12967-019-1937-9] [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: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Background SWATH-MS has emerged as the strategy of choice for biomarker discovery due to the proteome coverage achieved in acquisition and provision to re-interrogate the data. However, in quantitative analysis using SWATH, each sample from the comparison group is run individually in mass spectrometer and the resulting inter-run variation may influence relative quantification and identification of biomarkers. Normalization of data to diminish this variation thereby becomes an essential step in SWATH data processing. In most reported studies, data normalization methods used are those provided in instrument-based data analysis software or those used for microarray data. This study, for the first time provides an experimental evidence for selection of normalization method optimal for biomarker identification. Methods The efficiency of 12 normalization methods to normalize SWATH-MS data was evaluated based on statistical criteria in ‘Normalyzer’—a tool which provides comparative evaluation of normalization by different methods. Further, the suitability of normalized data for biomarker discovery was assessed by evaluating the clustering efficiency of differentiators, identified from the normalized data based on p-value, fold change and both, by hierarchical clustering in Genesis software v.1.8.1. Results Conventional statistical criteria identified VSN-G as the optimal method for normalization of SWATH data. However, differentiators identified from VSN-G normalized data failed to segregate test and control groups. We thus assessed data normalized by eleven other methods for their ability to yield differentiators which segregate the study groups. Datasets in our study demonstrated that differentiators identified based on p-value from data normalized with Loess-R stratified the study groups optimally. Conclusion This is the first report of experimentally tested strategy for SWATH-MS data processing with an emphasis on identification of clinically relevant biomarkers. Normalization of SWATH-MS data by Loess-R method and identification of differentiators based on p-value were found to be optimal for biomarker discovery in this study. The study also demonstrates the need to base the choice of normalization method on the application of the data. Electronic supplementary material The online version of this article (10.1186/s12967-019-1937-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mythreyi Narasimhan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Sadhana Kannan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Atanu Bhattacharjee
- Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Rukmini Govekar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India. .,BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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18
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Kuo YH, Shiau AL, Tung CL, Su YC, Li CF, Su BH, Tsao CJ, Wu CL, Feng YH, Wu P. Expression of prothymosin α in lung cancer is associated with squamous cell carcinoma and smoking. Oncol Lett 2019; 17:5740-5746. [PMID: 31105795 DOI: 10.3892/ol.2019.10248] [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: 03/24/2018] [Accepted: 01/11/2019] [Indexed: 11/06/2022] Open
Abstract
Prothymosin α (ProTα) is a nuclear protein that serves a role in oncogenesis, by promoting proliferation and inhibiting apoptosis in various malignancies. The present study was designed to investigate ProTα expression in resected human non-small cell lung cancer to define the clinicopathological associations of ProTα-positive lung cancer. Immunohistochemical staining of ProTα was performed using tumor sample slides from 149 patients with non-small cell lung cancer, who underwent surgical resection. Association between the expression of ProTα and the following clinicopathological parameters was accessed: Age, sex, stage, lymph node involvement, pathological subtype, recurrence and cigarette smoking. A total of 85 tumors (57%) were classified as ProTα-positive lung cancer by staining intensity and 73 tumors (49%) were regarded as ProTα-positive by scoring index. The majority of patients with ProTα-positive tumors were younger (P=0.05) and had squamous cell carcinoma (P<0.01) compared with older and adenocarcinoma. Positive expression of ProTα by staining intensity was associated with a higher incidence rate of cancer recurrence (P=0.05) compared with negative ProTα expression. ProTα was also associated with cigarette smoking, particularly in the group with squamous cell carcinoma. Therefore, the present data suggested that ProTα-positive non-small cell lung cancer was associated with younger patients, squamous cell carcinoma, cigarette smoking and a higher incidence recurrence rate, subsequently indicating a subtype consisting of patients with smoking-associated inferior outcomes.
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Affiliation(s)
- Yu-Hsuan Kuo
- Division of Hematology and Oncology, Department of Internal Medicine, Chi-Mei Medical Center, Tainan 71004, Taiwan, R.O.C.,College of Pharmacy and Science, Chia Nan University, Tainan 71710, Taiwan, R.O.C
| | - Ai-Li Shiau
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 70101, Taiwan, R.O.C
| | - Chao-Ling Tung
- Division of Hematology and Oncology, Department of Internal Medicine, Chi-Mei Medical Center, Tainan 71004, Taiwan, R.O.C
| | - Yu-Chu Su
- Department of Otolaryngology, National Cheng Kung University Hospital, Medical College, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C
| | - Chien-Feng Li
- Department of Pathology, Chi-Mei Medical Center, Yong Kang, Tainan 71004, Taiwan, R.O.C
| | - Bing-Hua Su
- Department of Biochemistry and Molecular Biology, National Cheng Kung University Medical College, Tainan 70101, Taiwan, R.O.C
| | - Chao-Jung Tsao
- Division of Hematology and Oncology, Chi-Mei Medical Center, Tainan 73657, Taiwan, R.O.C
| | - Chao-Liang Wu
- Department of Biochemistry and Molecular Biology, National Cheng Kung University Medical College, Tainan 70101, Taiwan, R.O.C
| | - Yin-Hsun Feng
- Division of Hematology and Oncology, Department of Internal Medicine, Chi-Mei Medical Center, Tainan 71004, Taiwan, R.O.C.,Department of Nursing, Chung Hwa University of Medical Technology, Tainan 71703, Taiwan, R.O.C
| | - Pensee Wu
- Institute of Reproductive and Developmental Biology, Imperial College London, London W12 ONN, UK
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Wu X, Zhang ZX, Chen XY, Xu YL, Yin N, Yang J, Zhu DM, Li DC, Zhou J. A Panel of Three Biomarkers Identified by iTRAQ for the Early Diagnosis of Pancreatic Cancer. Proteomics Clin Appl 2019; 13:e1800195. [PMID: 31025496 DOI: 10.1002/prca.201800195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/21/2019] [Indexed: 11/10/2022]
Abstract
PURPOSE Due to a lack of early diagnostic markers, pancreatic cancer (PC) remains a lethal disease. Proteomic approaches are now being applied to identify novel PC biomarkers. EXPERIMENTAL DESIGN In this study, iTRAQ and LC-MS/MS are used to perform comparative analyses of serum from PC patients and healthy controls (HC), to identify specific serum biomarkers for PC. Serum levels of candidate proteins are determined using ELISA. RESULTS Among 869 proteins identified, 55 are potential biomarkers; Vitamin K-dependent protein Z (PROZ) and tumor necrosis factor receptor superfamily member 6b (TNFRSF6B) are selected for further analysis. Serum levels of PROZ and TNFRSF6B are significantly higher in PC patients than in HC or pancreatic benign controls (BC) (p < 0.01). The AUCs range from 0.816 to 0.971 for PROZ, TNFRSF6B, and carbohydrate antigen 19-9, either individually or in combination, in PC versus HC+BC, and from 0.711 to 0.932 in PC Stage I versus HC+BC. CONCLUSIONS AND CLINICAL RELEVANCE It is demonstrated that PROZ and TNFRSF6B are novel serum biomarkers for detecting early stage PC, and for distinguishing PC from pancreatic benign tumor and healthy individuals. Additional large cohort studies are needed to develop PROZ and TNFRSF6B as clinical PC biomarkers.
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Affiliation(s)
- Xing Wu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Zi-Xiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.,Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Xing-Yu Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Ya-Ling Xu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Ni Yin
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Yang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.,Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Dong-Ming Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.,Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - De-Chun Li
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.,Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.,Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
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20
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Vanichtantikul A, Hodge KG, Somparn P, Saethang T, Triratanachat S, Pisitkun T, Lertkhachonsuk R. Proteomic identification of predictive biomarkers for malignant transformation in complete hydatidiform moles. Placenta 2019; 77:58-64. [PMID: 30827356 DOI: 10.1016/j.placenta.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/11/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Protein expression in cells are associated with oncogenesis. This study aims to explore proteomic profiles and discover potential biomarkers that can predict malignant transformation of hydatidiform mole. METHODS Retrospective analysis was done in 14 cases of remission hydatidiform mole and 14 cases of hydatidiform mole who later developed malignancy (GTN group). Molar tissues were retrieved from -70 °C frozen tissue. Subsequently, a large-scale proteomic analysis was performed to identify proteins and compare their abundance levels in the preserved molar tissues from these two groups using a dimethyl-labeling technique coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS A total of 2,153 proteins were identified from all samples. 22 and 10 proteins were significantly up-regulated and down-regulated, respectively, in the GTN group compared with the mole group. These altered proteins were found in several biological groups such as cell-cell adhesion, secreted proteins, and ribonucleoproteins. Several hormone-related proteins were among the most up-regulated proteins in the GTN group including choriogonadotropin subunit beta (β-hCG) and alpha (α-hCG), growth/differentiation factor 15, as well as both pregnancy-specific beta-1-glycoproteins 2 and 3. In contrast, protein S100-A11 and l-lactate dehydrogenase A chain, were down-regulated in molar tissue from most patients in the GTN group. DISCUSSION This study identified a set of differentially expressed proteins in molar tissues that could potentially be further examined as predictive biomarkers for the malignant transformation of CHMs. A molar proteome database was constructed and can be accessible online at http://sysbio.chula.ac.th/Database/GTD_DB/Supplementary_Data.xlsx.
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Affiliation(s)
- Asama Vanichtantikul
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Kenneth G Hodge
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Poorichaya Somparn
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Thammakorn Saethang
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Surang Triratanachat
- Division of Gynecologic Cytopathology, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Trairak Pisitkun
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Ruangsak Lertkhachonsuk
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand.
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21
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Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. PLoS One 2019; 14:e0208646. [PMID: 30615629 PMCID: PMC6322741 DOI: 10.1371/journal.pone.0208646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
To understand drug combination effect, it is necessary to decipher the interactions between drug targets-many of which are signaling molecules. Previously, such signaling pathway models are largely based on the compilation of literature data from heterogeneous cellular contexts. Indeed, de novo reconstruction of signaling interactions from large-scale molecular profiling is still lagging, compared to similar efforts in transcriptional and protein-protein interaction networks. To address this challenge, we introduce a novel algorithm for the systematic inference of protein kinase pathways, and applied it to published mass spectrometry-based phosphotyrosine profile data from 250 lung adenocarcinoma (LUAD) samples. The resulting network includes 43 TKs and 415 inferred, LUAD-specific substrates, which were validated at >60% accuracy by SILAC assays, including "novel' substrates of the EGFR and c-MET TKs, which play a critical oncogenic role in lung cancer. This systematic, data-driven model supported drug response prediction on an individual sample basis, including accurate prediction and validation of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either gene, thus contributing to current precision oncology efforts.
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Affiliation(s)
- Mukesh Bansal
- Psychogenics Inc., Paramus, New Jersey, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jing He
- Department of Systems Biology, Columbia University, New York, NY, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, United States of America
- Department of Biomedical Informatics (DBMI), Columbia University, New York, NY, United States of America
| | - Michael Peyton
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Manjunath Kustagi
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Archana Iyer
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Michael Comb
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, United States of America
| | - Michael White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Pharmacology, and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, United States of America
- Department of Biomedical Informatics (DBMI), Columbia University, New York, NY, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States of America
- Institute for Cancer Genetics, Columbia University, New York, NY, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States of America
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22
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Belczacka I, Latosinska A, Metzger J, Marx D, Vlahou A, Mischak H, Frantzi M. Proteomics biomarkers for solid tumors: Current status and future prospects. MASS SPECTROMETRY REVIEWS 2019; 38:49-78. [PMID: 29889308 DOI: 10.1002/mas.21572] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Cancer is a heterogeneous multifactorial disease, which continues to be one of the main causes of death worldwide. Despite the extensive efforts for establishing accurate diagnostic assays and efficient therapeutic schemes, disease prevalence is on the rise, in part, however, also due to improved early detection. For years, studies were focused on genomics and transcriptomics, aiming at the discovery of new tests with diagnostic or prognostic potential. However, cancer phenotypic characteristics seem most likely to be a direct reflection of changes in protein metabolism and function, which are also the targets of most drugs. Investigations at the protein level are therefore advantageous particularly in the case of in-depth characterization of tumor progression and invasiveness. Innovative high-throughput proteomic technologies are available to accurately evaluate cancer formation and progression and to investigate the functional role of key proteins in cancer. Employing these new highly sensitive proteomic technologies, cancer biomarkers may be detectable that contribute to diagnosis and guide curative treatment when still possible. In this review, the recent advances in proteomic biomarker research in cancer are outlined, with special emphasis placed on the identification of diagnostic and prognostic biomarkers for solid tumors. In view of the increasing number of screening programs and clinical trials investigating new treatment options, we discuss the molecular connections of the biomarkers as well as their potential as clinically useful tools for diagnosis, risk stratification and therapy monitoring of solid tumors.
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Affiliation(s)
- Iwona Belczacka
- Mosaiques-Diagnostics GmbH, Hannover, Germany
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | | | | | - David Marx
- Hôpitaux Universitaires de Strasbourg, Service de Transplantation Rénale, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), University of Strasbourg, National Center for Scientific Research (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC) UMR 7178, Strasbourg, France
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
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23
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Sreekumar VN. Global Scenario of Research in Oral Cancer. J Maxillofac Oral Surg 2018; 18:354-359. [PMID: 31371873 DOI: 10.1007/s12663-018-1166-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 10/10/2018] [Indexed: 10/28/2022] Open
Abstract
Introduction With 300,000 new cases diagnosed worldwide, oral cancer continues to be a major global public threat. In Indian subcontinent, oral cancer accounts for 30-40% of all cancer types. Methodology Early detection of oral cancer is still considered as the most effective way to improve survival. In this regard, early detection of oral premalignant lesions and conditions is quite important as it may help in prevention of oral cancer. Scientific evidence is available which clearly indicates that transition from normal epithelium to premalignancy to oral carcinoma is the result of accumulation of genetic and epigenetic alterations in a multi-step process. Conclusion Proper oral screening and understanding of the genetic and environmental factors involved in oral carcinogenesis will allow the emphasis of cancer medicine to shift from the therapy of established oral cancer to the prevention of oral carcinogenesis.
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Affiliation(s)
- Vinod Nair Sreekumar
- Department of Oral and Maxillofacial Surgery, P.M.S College of Dental Sciences and Research, Kerala University of Health Sciences, Trivandrum, India
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24
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Nikitakis NG, Pentenero M, Georgaki M, Poh CF, Peterson DE, Edwards P, Lingen M, Sauk JJ. Molecular markers associated with development and progression of potentially premalignant oral epithelial lesions: Current knowledge and future implications. Oral Surg Oral Med Oral Pathol Oral Radiol 2018; 125:650-669. [DOI: 10.1016/j.oooo.2018.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/21/2022]
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25
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Differential expression of peroxiredoxin 3 in laryngeal squamous cell carcinoma. Oncotarget 2018; 8:3471-3480. [PMID: 27966448 PMCID: PMC5356896 DOI: 10.18632/oncotarget.13838] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/22/2016] [Indexed: 02/05/2023] Open
Abstract
Peroxiredoxin (PRDX) proteins are involved in carcinogenesis. PRDX3, which is predominantly localized in mitochondria and up-regulated in several human cancers, seems to confer increased treatment resistance and aggressive phenotypes. This study examined the expression profile of PRDX3 and its possible clinical value in laryngeal squamous cell carcinoma (LSCC). The expression of PRDX3 in LSCC samples was confirmed by Western blotting and further analyzed by immunohistochemistry in LSCC samples of different clinical pathological stages. The results showed that up-regulated expression of PRDX3 was observed in LSCC and associated with poor differentiation (P < 0.01), primary tumor location, N category and tumor stage (P < 0.05). Knockdown of PRDX3 in the Hep-2 laryngeal carcinoma epithelial cell line significantly enhanced Hep-2 cells’ apoptosis and inhibited their proliferation and migration. Taken together, our results suggest that PRDX3 has substantial clinical impact on the progression of LSCC and shed new light on the role of PRDX3 in treatment resistance and aggressive phenotypes in LSCC.
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26
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Xiao C, Wu Q, Xie Y, Tan J, Ding Y, Bai L. Hypoglycemic mechanisms of Ganoderma lucidum polysaccharides F31 in db/db mice via RNA-seq and iTRAQ. Food Funct 2018; 9:6495-6507. [DOI: 10.1039/c8fo01656a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This study provides insight into the system-level hypoglycemic mechanisms of Ganoderma lucidum polysaccharides F31 by the integrative analysis of transcriptomics and proteomics data.
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Affiliation(s)
- Chun Xiao
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Open Laboratory of Applied Microbiology
- Guangdong Institute of Microbiology
- Guangzhou 510070
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Open Laboratory of Applied Microbiology
- Guangdong Institute of Microbiology
- Guangzhou 510070
| | - Yizhen Xie
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Open Laboratory of Applied Microbiology
- Guangdong Institute of Microbiology
- Guangzhou 510070
| | - Jianbin Tan
- Department of Toxicology
- Center for Disease Control and Prevention of Guangdong Province
- Guangzhou 510020
- China
| | - YinRun Ding
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Open Laboratory of Applied Microbiology
- Guangdong Institute of Microbiology
- Guangzhou 510070
| | - Lijuan Bai
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Open Laboratory of Applied Microbiology
- Guangdong Institute of Microbiology
- Guangzhou 510070
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27
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Chowdhury S, Veyhl J, Jessa F, Polyakova O, Alenzi A, MacMillan C, Ralhan R, Walfish PG. Programmed death-ligand 1 overexpression is a prognostic marker for aggressive papillary thyroid cancer and its variants. Oncotarget 2017; 7:32318-28. [PMID: 27086918 PMCID: PMC5078015 DOI: 10.18632/oncotarget.8698] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 01/05/2023] Open
Abstract
Programmed death-ligand 1(PD-L1) expression on tumor cells is emerging as a potential predictive biomarker in anti-PD-L1 directed cancer immunotherapy. We analyzed PD-L1 expression in papillary thyroid carcinoma (PTC) and its variants and determined its prognostic potential to predict clinical outcome in these patients. This study was conducted at an academic oncology hospital which is a prime referral centre for thyroid diseases. Immunohistochemical subcellular localization (IHC) analyses of PD-L1 protein was retrospectively performed on 251 archived formalin fixed and paraffin embedded (FFPE) surgical tissues (66 benign thyroid nodules and 185 PTCs) using a rabbit monoclonal anti-PD-L1 antibody (E1L3N, Cell Signaling Technology) and detected using VECTASTAIN rapid protocol with diaminobenzidine (DAB) as the chromogen. The clinical-pathological factors and disease outcome over 190 months were assessed; immunohistochemical subcellular localization of PD-L1 was correlated with disease free survival (DFS) using Kaplan Meier survival and Cox multivariate regression analysis. Increased PD-L1 immunostaining was predominantly localized in cytoplasm and occasionally in plasma membrane of tumor cells. Among all combined stages of PTC, patients with increased PD-L1 membrane or cytoplasmic positivity had significantly shorter median DFS (36 months and 49 months respectively) as compared to those with PD-L1 negative tumors (DFS, both 186 months with p < 0.001 and p < 0.01 respectively). Comparison of PD-L1+ and PD-L1− patients with matched staging showed increased cytoplasmic positivity in all four stages of PTC that correlated with a greater risk of recurrence and a poor prognosis, but increased membrane positivity significantly correlated with a greater risk of metastasis or death only in Stage IV patients. In conclusion, PD-L1 positive expression in PTC correlates with a greater risk of recurrence and shortened disease free survival supporting its potential application as a prognostic marker for PTC.
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Affiliation(s)
- Subrata Chowdhury
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Joe Veyhl
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Fatima Jessa
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Olena Polyakova
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Medicine, Endocrine Division, Mount Sinai Hospital and University of Toronto Medical School, Toronto, Ontario, Canada
| | - Ahmed Alenzi
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Medicine, Endocrine Division, Mount Sinai Hospital and University of Toronto Medical School, Toronto, Ontario, Canada
| | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ranju Ralhan
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada.,Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Paul G Walfish
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada.,Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Medicine, Endocrine Division, Mount Sinai Hospital and University of Toronto Medical School, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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28
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Chen Z, Long L, Wang K, Cui F, Zhu L, Tao Y, Wu Q, Xiang M, Liang Y, Qiu S, Xiao Z, Yi B. Identification of nasopharyngeal carcinoma metastasis-related biomarkers by iTRAQ combined with 2D-LC-MS/MS. Oncotarget 2017; 7:34022-37. [PMID: 27145374 PMCID: PMC5085135 DOI: 10.18632/oncotarget.9067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/16/2016] [Indexed: 12/15/2022] Open
Abstract
To identify metastasis-related proteins in nasopharyngeal carcinoma (NPC), iTRAQ-tagging combined with 2D LC-MS/MS analysis was performed to identify the differentially expressed proteins (DEPs) in high metastatic NPC 5-8F cells and non-metastatic NPC 6-10B cells, and qRT-PCR and Western blotting were used to confirm DEPs. As a result, 101 DEPs were identified by proteomics, and 12 DEPs were selectively validated. We further detected expression of three DEPs (RAN, SQSTM1 and TRIM29) in a cohort of NPC tissue specimens to assess their value as NPC metastatic biomarkers, and found that combination of RAN, SQSTM1 and TRIM29 could discriminate metastatic NPC from non-metastatic NPC with a sensitivity of 88% and a specificity of 91%. TRIM29 and RAN expression level were closely correlated with lymph node and distant metastasis and clinical stage (P <0.05) in NPC patients. Finally, a combination of loss-of-function and gain-of-function approaches was performed to determine the effects of TRIM29 on NPC cell proliferation, migration, invasion and metastasis. The results showed that TRIM29 knockdown significantly attenuated while TRIM29 overexpression promoted NPC cell in vitro proliferation, migration and invasion and in vivo metastasis. The present data first time show that SQSTM1, RAN and TRIM29 are novel potential biomarkers for predicting NPC metastasis, demonstrate that TRIM29 is a metastasis-promoted protein of NPC.
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Affiliation(s)
- Zhen Chen
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lu Long
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Kun Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Facai Cui
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lepan Zhu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Ya Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Qiong Wu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Manlin Xiang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yunlai Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Shiyang Qiu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Zhiqiang Xiao
- The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Yi
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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29
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Aghajani MJ, Yang T, McCafferty CE, Graham S, Wu X, Niles N. Predictive relevance of programmed cell death protein 1 and tumor-infiltrating lymphocyte expression in papillary thyroid cancer. Surgery 2017; 163:130-136. [PMID: 29128181 DOI: 10.1016/j.surg.2017.04.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/22/2017] [Accepted: 04/08/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Co-signaling molecule programmed cell death 1 ligand 1 has been shown to induce potent inhibition of T cell-mediated antitumoral immunity. Our study aimed to investigate the prognostic value of programmed cell death 1 ligand 1 expression and tumor-infiltrating lymphocyte density as biomarkers in specimens from patients with papillary thyroid cancer. METHODS We retrospectively analyzed the data and tissue samples of 75 patients with papillary thyroid cancer. Stained cells were counted manually and analyzed for clinical and histopathologic correlations and disease-free survival. RESULTS Programmed cell death 1 ligand 1 expression was significantly correlated with increased incidence of lymphovascular invasion (P = .038), extrathyroidal extension (P = .026), and concurrent lymphocytic thyroiditis (P = .003). Patients with low CD8+ and CD3+ expression presented with a significantly higher incidence of lymph node metastasis (P = .042) and extrathyroidal extension (P = .015). The subgroup of cases with positive programmed cell death 1 ligand 1 expression and low CD8+ T cell infiltration demonstrated a significantly increased incidence of lymph node metastasis (P = .031). Univariate and multivariate analysis confirmed that a high CD8+ T cell density was significantly associated with favorable disease-free survival (P = .017). Subanalysis revealed that the shortest disease-free survival was evident in the programmed cell death 1 ligand 1+/CD8low group (P = .004). CONCLUSION Our findings indicate that CD8+ tumor-infiltrating lymphocyte density and programmed cell death 1 ligand 1 expression may serve as valuable predictive biomarkers in patients with papillary thyroid cancer.
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Affiliation(s)
- Marra J Aghajani
- Thyroid Cancer Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW, Australia.
| | - Tao Yang
- Thyroid Cancer Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW, Australia; SydPath, Saint Vincent's Hospital, Sydney, NSW, Australia
| | | | - Susannah Graham
- Thyroid Cancer Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW, Australia; Department of Head & Neck Surgery, Liverpool Hospital, Liverpool, NSW, Australia
| | - Xiaojuan Wu
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW, Australia
| | - Navin Niles
- Thyroid Cancer Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW, Australia; Department of Head & Neck Surgery, Liverpool Hospital, Liverpool, NSW, Australia
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30
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Xu JW, Li YL, Zhang SJ, Yang WQ, Nie WT, Jiang HQ. Quantitative Serum Proteomic Analysis of Essential Hypertension Using iTRAQ Technique. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6761549. [PMID: 29201909 PMCID: PMC5671681 DOI: 10.1155/2017/6761549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
Abstract
Essential hypertension (EH) is a risk factor for some severe diseases. This study aimed to screen out serum special proteins and seek interaction between them, which would provide new therapeutic targets and elucidate the comprehensive pathophysiological mechanism for EH. Patients with EH (Group A, n = 47) and healthy controls (HC) (Group B, n = 47) were recruited in this study. Serums from the two groups were analyzed with isobaric tags for relative and absolute quantitation coupled two-dimensional liquid chromatography followed by electrospray ionization-tandem mass spectrometry technique, while the candidate special proteins were verified with ELISA and western blot. A total of 404 proteins were identified, of which 30 proteins were upregulated (>1.2-fold, p < 0.05) and 81 proteins were downregulated (<0.833-fold, p < 0.05) compared with HC group. With GO, KEGG analysis, and literature retrieval, 4 proteins, cathepsin G, transforming growth factor beta-1, hyaluronidase-1, and kininogen-1, were found jointly involved in the renin-angiotensin-aldosterone system and kallikrein-kinin system. The profiles of these 4 candidate proteins were confirmed with ELISA and western blot. The concentration variation of these 4 proteins could better predict the occurrence and illustrate the pathophysiological mechanism of EH. And their discovery may help pave the way for exploring new therapies of EH.
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Affiliation(s)
- Jing-Wen Xu
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong Academy of Medical Sciences, 38 Shadowless Hill Road, Tianqiao District, Jinan, Shandong Province, China
| | - Yun-Lun Li
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, Shandong Province, China
| | - Shi-Jun Zhang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Wen-Qing Yang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Wen-Ting Nie
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Hai-Qiang Jiang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
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31
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Hwang JT, Gu YR, Dickson BJ, Shen M, Ralhan R, Walfish PG, Mock D, Pritzker KP. RETRACTED: Straticyte demonstrates prognostic value over oral epithelial dysplasia grade for oral potentially malignant lesion assessment. Oral Oncol 2017; 72:1-6. [DOI: 10.1016/j.oraloncology.2017.06.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 12/29/2022]
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32
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Hsiao YC, Chi LM, Chien KY, Chiang WF, Chen SF, Chuang YN, Lin SY, Wu CC, Chang YT, Chu LJ, Chen YT, Chia SL, Chien CY, Chang KP, Chang YS, Yu JS. Development of a Multiplexed Assay for Oral Cancer Candidate Biomarkers Using Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry. Mol Cell Proteomics 2017; 16:1829-1849. [PMID: 28821604 DOI: 10.1074/mcp.ra117.000147] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Oral cancer is one of the most common cancers worldwide, and there are currently no biomarkers approved for aiding its management. Although many potential oral cancer biomarkers have been discovered, very few have been verified in body fluid specimens in parallel to evaluate their clinical utility. The lack of appropriate multiplexed assays for chosen targets represents one of the bottlenecks to achieving this goal. In the present study, we develop a peptide immunoaffinity enrichment-coupled multiple reaction monitoring-mass spectrometry (SISCAPA-MRM) assay for verifying multiple reported oral cancer biomarkers in saliva. We successfully produced 363 clones of mouse anti-peptide monoclonal antibodies (mAbs) against 36 of 49 selected targets, and characterized useful mAbs against 24 targets in terms of their binding affinity for peptide antigens and immuno-capture ability. Comparative analyses revealed that an equilibrium dissociation constant (KD ) cut-off value < 2.82 × 10-9 m could identify most clones with an immuno-capture recovery rate >5%. Using these mAbs, we assembled a 24-plex SISCAPA-MRM assay and optimized assay conditions in a 25-μg saliva matrix background. This multiplexed assay showed reasonable precision (median coefficient of variation, 7.16 to 32.09%), with lower limits of quantitation (LLOQ) of <10, 10-50, and >50 ng/ml for 14, 7 and 3 targets, respectively. When applied to a model saliva sample pooled from oral cancer patients, this assay could detect 19 targets at higher salivary levels than their LLOQs. Finally, we demonstrated the utility of this assay for quantification of multiple targets in individual saliva samples (20 healthy donors and 21 oral cancer patients), showing that levels of six targets were significantly altered in cancer compared with the control group. We propose that this assay could be used in future studies to compare the clinical utility of multiple oral cancer biomarker candidates in a large cohort of saliva samples.
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Affiliation(s)
- Yung-Chin Hsiao
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Lang-Ming Chi
- ¶Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Yi Chien
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,¶Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Fan Chiang
- **Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan.,‡‡School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Szu-Fan Chen
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yao-Ning Chuang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Yu Lin
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chun Wu
- ‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Ting Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yi-Ting Chen
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,§§Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,¶¶Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shu-Li Chia
- ‖‖Health Promotion Administration, Ministry of Health and Welfare, Taiwan
| | - Chih-Yen Chien
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Ping Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jau-Song Yu
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; .,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Identification of Tengfu Jiangya Tablet Target Biomarkers with Quantitative Proteomic Technique. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7594805. [PMID: 28408942 PMCID: PMC5376940 DOI: 10.1155/2017/7594805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/08/2017] [Indexed: 12/21/2022]
Abstract
Tengfu Jiangya Tablet (TJT) is a well accepted antihypertension drug in China and its major active components were Uncaria total alkaloids and Semen Raphani soluble alkaloid. To further explore treatment effects mechanism of TJT on essential hypertension, a serum proteomic study was performed. Potential biomarkers were quantified in serum of hypertension individuals before and after taking TJT with isobaric tags for relative and absolute quantitation (iTRAQ) coupled two-dimensional liquid chromatography followed electrospray ionization-tandem mass spectrometry (2D LC-MS/MS) proteomics technique. Among 391 identified proteins with high confidence, 70 proteins were differentially expressed (fold variation criteria, >1.2 or <0.83) between two groups (39 upregulated and 31 downregulated). Combining with Gene Ontology annotation, KEGG pathway analysis, and literature retrieval, 5 proteins were chosen as key target biomarkers during TJT therapeutic process. And the alteration profiles of these 5 proteins were verified by ELISA and Western Blot. Proteins Kininogen 1 and Keratin 1 are members of Kallikrein system, while Myeloperoxidase, Serum Amyloid protein A, and Retinol binding protein 4 had been reported closely related to vascular endothelial injury. Our study discovered 5 target biomarkers of the compound Chinese medicine TJT. Secondly, this research initially revealed the antihypertension therapeutic mechanism of this drug from a brand-new aspect.
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Li G, Li M, Liang X, Xiao Z, Zhang P, Shao M, Peng F, Chen Y, Li Y, Chen Z. Identifying DCN and HSPD1 as Potential Biomarkers in Colon Cancer Using 2D-LC-MS/MS Combined with iTRAQ Technology. J Cancer 2017; 8:479-489. [PMID: 28261350 PMCID: PMC5332900 DOI: 10.7150/jca.17192] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/29/2016] [Indexed: 12/31/2022] Open
Abstract
Colon cancer is one of the most common types of gastrointestinal cancers and the fourth cause of cancer death worldwide. To discover novel diagnostic biomarkers for colon cancer and investigate potential mechanisms of oncogenesis, quantitative proteomic approach using iTRAQ-tagging and 2D-LC-MS/MS was performed to characterize proteins alterations in colon cancer and non-neoplastic colonic mucosa (NNCM) using laser capture microdissection-harvested from the two types of tissues, respectively. As a result, 188 DEPs were identified, and the differential expression of two DEPs (DCN and HSPD1) was further verified by Western blotting and immunohistochemistry. KEGG pathway analysis disclosed that the DEPs were related to signaling pathways associated with cancer; furthermore, DCN and HSPD1 are in the relative central hub position among protein-protein interaction subnetwork of the DEPs. The results not only shed light on the mechanism by the DEPs contributed to colonic carcinogenesis, but also showed that DCN and HSPD1 are novel potential biomarkers for the diagnosis of colon cancer.
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Affiliation(s)
- Guoqing Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmacy and Life Science, University of South China, Hengyang 421001, Hunan, China
| | - Maoyu Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xujun Liang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhefeng Xiao
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Pengfei Zhang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Meiying Shao
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Fang Peng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanyuan Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.; Medical College, Guangxi University of Science and Technology, Liuzhou 545005, Guangxi, China
| | - Zhuchu Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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Proteomic assessment of colorectal cancers and respective resection margins from patients of the Amazon state of Brazil. J Proteomics 2017; 154:59-68. [DOI: 10.1016/j.jprot.2016.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/25/2016] [Accepted: 12/12/2016] [Indexed: 12/11/2022]
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Kailemia MJ, Park D, Lebrilla CB. Glycans and glycoproteins as specific biomarkers for cancer. Anal Bioanal Chem 2017; 409:395-410. [PMID: 27590322 PMCID: PMC5203967 DOI: 10.1007/s00216-016-9880-6] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
Abstract
Protein glycosylation and other post-translational modifications are involved in potentially all aspects of human growth and development. Defective glycosylation has adverse effects on human physiological conditions and accompanies many chronic and infectious diseases. Altered glycosylation can occur at the onset and/or during tumor progression. Identifying these changes at early disease stages may aid in making decisions regarding treatments, as early intervention can greatly enhance survival. This review highlights some of the efforts being made to identify N- and O-glycosylation profile shifts in cancer using mass spectrometry. The analysis of single or panels of potential glycoprotein cancer markers are covered. Other emerging technologies such as global glycan release and site-specific glycosylation analysis and quantitation are also discussed. Graphical Abstract Steps involved in the biomarker discovery.
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Affiliation(s)
- Muchena J Kailemia
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Dayoung Park
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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Dong LY, Zhou WZ, Ni JW, Xiang W, Hu WH, Yu C, Li HY. Identifying the optimal gene and gene set in hepatocellular carcinoma based on differential expression and differential co-expression algorithm. Oncol Rep 2016; 37:1066-1074. [DOI: 10.3892/or.2016.5333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/10/2016] [Indexed: 11/06/2022] Open
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Individualized five-year risk assessment for oral premalignant lesion progression to cancer. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 123:374-381. [PMID: 28110942 DOI: 10.1016/j.oooo.2016.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 11/03/2016] [Accepted: 11/13/2016] [Indexed: 12/23/2022]
Abstract
OBJECTIVE The standard of care for premalignant lesion risk assessment is dysplasia grading by histopathology. With significant overlap between dysplasia grades and high inter- and intraobserver variations, histopathology dysplasia grading alone is not a useful prognostic tool. Our aim is to investigate whether a method for quantitatively assessing S100A7, a prognostic biomarker, using image analysis can better predict clinical outcome in cases with oral dysplasia. STUDY DESIGN Using the Visiopharm image analysis system, we analyzed a cohort of 150 oral biopsy samples to build and test Straticyte, a model for individualized assessment of the 5-year risk of progression of oral precancerous lesions to invasive squamous cell carcinomas. RESULTS Straticyte classified lesions more accurately than histopathological dysplasia grading for risk to progression to cancer over the following 5 years. The sensitivity of low-risk versus intermediate- and high-risk Straticyte groups was 95% compared to 75% for mild versus moderate and severe dysplasia. Furthermore, the negative predictive value for low-risk versus intermediate- and high-risk Straticyte groups was 78% compared to 59% for mild versus moderate and severe dysplasia. CONCLUSION By quantitatively assessing S100A7, Straticyte better defines the risk for developing oral squamous cell carcinoma than histopathological dysplasia grading alone.
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Fan S, Zhang D, Lei C, Chen H, Xing L, Ma J, Zhao C, Han M. Proteome Analyses Using iTRAQ Labeling Reveal Critical Mechanisms in Alternate Bearing Malus prunifolia. J Proteome Res 2016; 15:3602-3616. [DOI: 10.1021/acs.jproteome.6b00357] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Lei
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongfei Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Juanjuan Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Somasundaram RT, Kaur J, Leong I, MacMillan C, Witterick IJ, Walfish PG, Ralhan R. Subcellular differential expression of Ep-ICD in oral dysplasia and cancer is associated with disease progression and prognosis. BMC Cancer 2016; 16:486. [PMID: 27421772 PMCID: PMC4947324 DOI: 10.1186/s12885-016-2507-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 06/20/2016] [Indexed: 01/25/2023] Open
Abstract
Background Identification of patients with oral dysplasia at high risk of cancer development and oral squamous cell carcinoma (OSCC) at increased risk of disease recurrence will enable rigorous personalized treatment. Regulated intramembranous proteolysis of Epithelial cell adhesion molecule (EpCAM) resulting in release of its intracellular domain Ep-ICD into cytoplasm and nucleus triggers oncogenic signaling. We analyzed the expression of Ep-ICD in oral dysplasia and cancer and determined its clinical significance in disease progression and prognosis. Methods In a retrospective study, immunohistochemical analysis of nuclear and cytoplasmic Ep-ICD and EpEx (extracellular domain of EpCAM), was carried out in 115 OSCC, 97 oral dysplasia and 105 normal oral tissues, correlated with clinicopathological parameters and disease outcome over 60 months for oral dysplasia and OSCC patients. Disease-free survival (DFS) was determined by Kaplan-Meier method and multivariate Cox regression analysis. Results In comparison with normal oral tissues, significant increase in nuclear Ep-ICD and membrane EpEx was observed in dysplasia, and OSCC (p = 0.013 and < 0.001 respectively). Oral dysplasia patients with increased overall Ep-ICD developed cancer in short time period (mean = 47 months; p = 0.044). OSCC patients with increased nuclear Ep-ICD and membrane EpEx had significantly reduced mean DFS of 33.7 months (p = 0.018). Conclusions Our study provided clinical evidence for Ep-ICD as a predictor of cancer development in patients with oral dysplasia and recurrence in OSCC patients, suggesting its potential utility in enhanced management of those patients detected to have increased risk of progression to cancer and recurrence in OSCC patients.
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Affiliation(s)
- Raj Thani Somasundaram
- Alex and Simona Shnaider Laboratory, Laboratory Medicine in Molecular Onocolgy, Mount Sinia Hospital, Room 6-318, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Jatinder Kaur
- Alex and Simona Shnaider Laboratory, Laboratory Medicine in Molecular Onocolgy, Mount Sinia Hospital, Room 6-318, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Iona Leong
- Department of Otolaryngology, Head and Neck Surgery, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, 600 University Avenue, 6-500, Toronto, ON, M5G 1X5, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ian J Witterick
- Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Otolaryngology - Head and Neck Surgery, Alex and Simona Shnaider Laboratory in Molecular Oncology, Mount Sinai Hospital, Joseph & Wolf Lebovic Health Complex, 600 University Avenue, 6-500, Toronto, ON, M5G 1X5, Canada.,Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Toronto, ON, M5G 2N2, Canada
| | - Paul G Walfish
- Alex and Simona Shnaider Laboratory, Laboratory Medicine in Molecular Onocolgy, Mount Sinia Hospital, Room 6-318, 600 University Avenue, Toronto, ON, M5G 1X5, Canada. .,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada. .,Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Toronto, ON, M5G 2N2, Canada. .,Department of Medicine, Endocrine Division, Mount Sinai Hospital and University of Toronto, Joseph & Wolf Lebovic Health Complex, Room 413-7, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.
| | - Ranju Ralhan
- Alex and Simona Shnaider Laboratory, Laboratory Medicine in Molecular Onocolgy, Mount Sinia Hospital, Room 6-318, 600 University Avenue, Toronto, ON, M5G 1X5, Canada. .,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada. .,Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology - Head and Neck Surgery, Alex and Simona Shnaider Laboratory in Molecular Oncology, Mount Sinai Hospital, Joseph & Wolf Lebovic Health Complex, 600 University Avenue, 6-500, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Toronto, ON, M5G 2N2, Canada.
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Kumar M, Mehra S, Thakar A, Shukla NK, Roychoudhary A, Sharma MC, Ralhan R, Chauhan SS. End Binding 1 (EB1) overexpression in oral lesions and cancer: A biomarker of tumor progression and poor prognosis. Clin Chim Acta 2016; 459:45-52. [PMID: 27208742 DOI: 10.1016/j.cca.2016.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Oral squamous cell carcinoma (OSCC) patients are at high risk of loco-regional recurrence and despite the improvement in treatment strategy, 5-year survival rates are about 50%. Identification of patients at high risk of recurrence may enable rigorous personalized post-treatment management. In an earlier proteomics study we observed overexpression of End Binding Protein (EB1) in OSCC. In the present study we investigated the diagnostic and prognostic significance of alterations in expression of EB1 in oral cancer. METHODS In this retrospective study, the expression of EB1 protein was evaluated in 259 OSCCs, 41 dysplasia, 166 hyperplasia and 126 normal tissues using immunohistochemistry and correlated with clinical-pathological parameters and prognosis of OSCC patients over a follow-up period of up to 91months. RESULTS Significantly higher expression of cytoplasmic EB1 was observed in hyperplasia [p<0.001, OR=7.2, 95% CI=4.1-12.8], dysplasia (p<0.001, OR=21.8, CI=8.8-50.2) and OSCCs (p<0.001, OR=10.1, CI=5.8-17.4) in comparison with normal mucosa. Univariate analysis revealed cytoplasmic EB1 association with tumor grade, tumor size and recurrence of the disease. Kaplan Meier survival analysis of EB1 expression showed significantly reduced disease free survival (DFS) (p=0.003). Notably, OSCC patients showing cytoplasmic EB1 overexpression demonstrated significantly reduced DFS (p=0.004, HR=2.1). CONCLUSION EB1 overexpression is an early event in oral tumorigenesis and cytoplasmic EB1 accumulation is associated with poor prognosis and tumor recurrence in OSCC patients.
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Affiliation(s)
- Manish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Siddharth Mehra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Alok Thakar
- Department of Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi, India
| | - Nootan Kumar Shukla
- Department of Surgery, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ajoy Roychoudhary
- Department of Dental Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ranju Ralhan
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital, Toronto, Ontario, Canada; Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology - Head and Neck Surgery, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Ontario, Canada.
| | - Shyam Singh Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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Yang H, Xiong X, Wang X, Tan B, Li T, Yin Y. Effects of Weaning on Intestinal Upper Villus Epithelial Cells of Piglets. PLoS One 2016; 11:e0150216. [PMID: 27022727 PMCID: PMC4811545 DOI: 10.1371/journal.pone.0150216] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/10/2016] [Indexed: 12/25/2022] Open
Abstract
The intestinal upper villus epithelial cells represent the differentiated epithelial cells and play key role in digesting and absorbing lumenal nutrients. Weaning stress commonly results in a decrease in villus height and intestinal dysfunction in piglets. However, no study have been conducted to test the effects of weaning on the physiology and functions of upper villus epithelial cells. A total of 40 piglets from 8 litters were weaned at 14 days of age and one piglet from each litter was killed at 0 d (w0d), 1 d (w1d), 3 d (w3d), 5 d (w5d), and 7 d (w7d) after weaning, respectively. The upper villus epithelial cells in mid-jejunum were isolated using the distended intestinal sac method. The expression of proteins in upper villus epithelial cells was analyzed using the isobaric tags for relative and absolute quantification or Western blotting. The expression of proteins involved in energy metabolism, Golgi vesicle transport, protein amino acid glycosylation, secretion by cell, transmembrane transport, ion transport, nucleotide catabolic process, translational initiation, and epithelial cell differentiation and apoptosis, was mainly reduced during the post-weaning period, and these processes may be regulated by mTOR signaling pathway. These results indicated that weaning inhibited various cellular processes in jejunal upper villus epithelial cells, and provided potential new directions for exploring the effects of weaning on the functions of intestine and improving intestinal functions in weaning piglets.
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Affiliation(s)
- Huansheng Yang
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
- School of Life Sciences, Hunan Normal University, Changsha, China
- Fujian Aonong Biotechnology Corporation, Xiamen, Fujian, China
| | - Xia Xiong
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
| | - Xiaocheng Wang
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
| | - Bie Tan
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
| | - Tiejun Li
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
| | - Yulong Yin
- Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan, China
- School of Life Sciences, Hunan Normal University, Changsha, China
- * E-mail:
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Matta A, Masui O, Siu KWM, Ralhan R. Identification of 14-3-3zeta associated protein networks in oral cancer. Proteomics 2016; 16:1079-89. [PMID: 26857332 DOI: 10.1002/pmic.201500489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 01/03/2023]
Abstract
Advancements in genomics, proteomics, and bioinformatics have improved our understanding of gene/protein networks involved in intra- and intercellular communication and tumor-host interactions. Using proteomics integrated with bioinformatics, previously we reported overexpression of 14-3-3ζ in premalignant oral lesions and oral squamous cell carcinoma tissues in comparison with normal oral epithelium. 14-3-3ζ emerged as a novel molecular target for therapeutics and a potential prognostic marker in oral squamous cell carcinoma patients. However, the role of 14-3-3ζ in development and progression of oral cancer is not known yet. This study aimed to identify the 14-3-3ζ associated protein networks in oral cancer cell lines using IP-MS/MS and bioinformatics. A total of 287 binding partners of 14-3-3ζ were identified in metastatic (MDA1986) and nonmetastatic (SCC4) oral cancer cell lines including other 14-3-3 isoforms (2%), proteins involved in apoptosis (2%), cytoskeleton (9%), metabolism (16%), and maintenance of redox potential (2%). Our bioinformatics analysis revealed involvement of 14-3-3ζ in protein networks regulating cell cycle, proliferation, apoptosis, cellular trafficking, and endocytosis in oral cancer. In conclusion, our data revealed several novel protein interaction networks involving 14-3-3ζ in oral cancer progression and metastasis.
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Affiliation(s)
- Ajay Matta
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada
| | - Olena Masui
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada
| | - K W Michael Siu
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada
| | - Ranju Ralhan
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, Canada.,Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, ON, Canada
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Wang Y, Xu L, Tang M, Jiang H, Chen W, Zhang W, Wang R, Liu L. Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure. FRONTIERS IN PLANT SCIENCE 2016; 7:1871. [PMID: 28018404 PMCID: PMC5156831 DOI: 10.3389/fpls.2016.01871] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/28/2016] [Indexed: 05/22/2023]
Abstract
Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L-1(Pb500) and 1000 mg L-1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included "cell wall," "apoplast," "response to metal ion," "vacuole," and "peroxidase activity," and the critical enriched pathways were involved in "citric acid (TCA) cycle and respiratory electron transport," "pyruvate metabolism," "phenylalanine metabolism," "phenylpropanoid biosynthesis," and "carbon metabolism." Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)-glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.
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Ralhan R, Veyhl J, Chaker S, Assi J, Alyass A, Jeganathan A, Somasundaram RT, MacMillan C, Freeman J, Vescan AD, Witterick IJ, Walfish PG. Immunohistochemical Subcellular Localization of Protein Biomarkers Distinguishes Benign from Malignant Thyroid Nodules: Potential for Fine-Needle Aspiration Biopsy Clinical Application. Thyroid 2015; 25:1224-34. [PMID: 26131603 DOI: 10.1089/thy.2015.0114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND It is of critical clinical importance to select accurately for surgery thyroid nodules at risk for malignancy and avoid surgery on those that are benign. Using alterations in subcellular localization for seven putative biomarker proteins (identified by proteomics), this study aimed to define a specific combination of proteins in surgical tissues that could distinguish benign from malignant nodules to assist in future surgical selection by fine-needle aspiration biopsy (FNAB). METHODS Immunohistochemical subcellular localization (IHC) analyses of seven proteins were retrospectively performed on surgical tissues (115 benign nodules and 114 papillary-based thyroid carcinomas [TC]), and a risk model biomarker panel was developed and validated. The biomarker panel efficacy was verified in 50 FNAB formalin-fixed and paraffin-embedded cell blocks, and 26 cytosmears were prepared from fresh surgically resected thyroid nodules. RESULTS Selection modeling using these proteins resulted in nuclear phosphoglycerate kinase 1 (PGK1) loss and nuclear Galectin-3 overexpression as the best combination for distinguishing TC from benign nodules (area under the curve [AUC] 0.96 and 0.95 in test and validation sets, respectively). A computed malignancy score also accurately identified TC in benign and indeterminate nodules (test and validation sets: AUC 0.94, 0.90; specificity 98%, 99%). Its efficacy was confirmed in surgical FNAB cell blocks and cytosmears. CONCLUSION Using surgical tissues, it was observed that a combination of PGK1 and Galectin-3 had high efficiency for distinguishing benign from malignant thyroid nodules and could improve surgical selection for TC among indeterminate nodules. Further validation in prospective preoperative FNAB will be required to confirm such a clinical application.
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Affiliation(s)
- Ranju Ralhan
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
- 2 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital , Toronto, Canada
- 3 Laboratory Medicine and Pathobiology, University of Toronto , Toronto, Canada
- 4 Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital , Toronto, Canada
- 5 Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital , Toronto, Canada
- 6 Department of Otolaryngology-Head and Neck Surgery, University of Toronto , Toronto, Canada
| | - Joe Veyhl
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Seham Chaker
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Jasmeet Assi
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Akram Alyass
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Ajitha Jeganathan
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Raj Thani Somasundaram
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
| | - Christina MacMillan
- 2 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital , Toronto, Canada
- 3 Laboratory Medicine and Pathobiology, University of Toronto , Toronto, Canada
| | - Jeremy Freeman
- 4 Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital , Toronto, Canada
- 5 Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital , Toronto, Canada
- 6 Department of Otolaryngology-Head and Neck Surgery, University of Toronto , Toronto, Canada
| | - Allan D Vescan
- 4 Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital , Toronto, Canada
- 5 Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital , Toronto, Canada
- 6 Department of Otolaryngology-Head and Neck Surgery, University of Toronto , Toronto, Canada
| | - Ian J Witterick
- 4 Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital , Toronto, Canada
- 5 Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital , Toronto, Canada
- 6 Department of Otolaryngology-Head and Neck Surgery, University of Toronto , Toronto, Canada
| | - Paul G Walfish
- 1 Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Mount Sinai Hospital , Toronto, Canada
- 2 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital , Toronto, Canada
- 3 Laboratory Medicine and Pathobiology, University of Toronto , Toronto, Canada
- 4 Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Department of Otolaryngology-Head and Neck Surgery Program, Mount Sinai Hospital , Toronto, Canada
- 7 Department of Medicine, Endocrine Division, Mount Sinai Hospital , Toronto, Canada
- 8 Department of Medicine, University of Toronto Medical School , Toronto, Canada
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Quantitative proteomic profiling of renal tissue in human chronic rejection biopsy samples after renal transplantation. Transplant Proc 2015; 47:323-31. [PMID: 25769567 DOI: 10.1016/j.transproceed.2014.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/29/2014] [Accepted: 10/05/2014] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Chronic rejection (CR) is the leading cause of late renal transplant failure and is characterized by a relatively slow but progressive loss of renal function in combination with proteinuria and hypertension >3 months after transplantation. To identify and quantify the protein profiles in renal tissues of CR patients, we used isotope tagging for relative and absolute quantification (iTRAQ)-based proteomic technology to perform global protein expression analyses in CR patients and control subjects. MATERIALS AND METHODS After protein extraction, quantitation, and digestion, samples were labeled with iTRAQ reagents and then separated by strong cation exchange and high-performance liquid chromatography. The fractions were further analyzed by tandem mass spectrometry. ProteinPilot version 4.0 software and the Swiss-Prot human database were applied for statistical analysis and database searching, respectively. Differentially expressed proteins were subjected to bioinformatic analysis by using the Gene Ontology database and the Kyoto Encyclopedia of Genes and Genomes database to further characterize their potential functional roles and related pathways in CR. RESULTS In total, 1857 distinct proteins (confidence >95%, ρ < .05) were identified and quantified. Using a strict cutoff value of 1.5-fold for expressed variation, 87 proteins showed significant differences in expression between the CR and control groups; 53 were up-regulated and 34 were down-regulated. The differentially expressed proteins were mainly involved in protein binding, structural molecule activity, and extracellular matrix structural constituent. Several proteins, such as the alpha-1 chain of collagen type IV and integrin alpha-1, may play roles in the pathogenesis of CR and were implicated in the extracellular matrix-receptor interaction pathway. CONCLUSIONS This study is the first to focus on iTRAQ-based quantitative proteomic characterization of renal tissue in CR. These insights may broaden our understanding of the molecular mechanisms underlying CR and provide potential biomarker candidates for future diagnostics.
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Liu T, Wu C, Jain MR, Nagarajan N, Yan L, Dai H, Cui C, Baykal A, Pan S, Ago T, Sadoshima J, Li H. Master redox regulator Trx1 upregulates SMYD1 & modulates lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1816-1822. [PMID: 26410624 DOI: 10.1016/j.bbapap.2015.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/02/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023]
Abstract
Thioredoxin 1 (Trx1) is а antioxidant protein that regulates protein disulfide bond reduction, transnitrosylation, denitrosylation and other redox post-translational modifications. In order to better understand how Trx1 modulates downstream protective cellular signaling events following cardiac ischemia, we conducted an expression proteomics study of left ventricles (LVs) after thoracic aortic constriction stress treatment of transgenic mice with cardiac-specific over-expression of Trx1, an animal model that has been proven to withstand more stress than its non-transgenic littermates. Although previous redox post-translational modifications proteomics studies found that several cellular protein networks are regulated by Trx1-mediated disulfide reduction and transnitrosylation, we found that Trx1 regulates the expression of a limited number of proteins. Among the proteins found to be upregulated in this study was SET and MYND domain-containing protein 1 (SMYD1), a lysine methyltransferase highly expressed in cardiac and other muscle tissues and an important regulator of cardiac development. The observation of SMYD1 induction by Trx1 following thoracic aortic constriction stress is consistent with the retrograde fetal gene cardiac protection hypothesis. The results presented here suggest for the first time that, in addition to being a master redox regulator of protein disulfide bonds and nitrosation, Trx1 may also modulate lysine methylation, a non-redox post-translational modification, via the regulation of SMYD1 expression. Such crosstalk between redox signaling and a non-redox PTM regulation may provide novel insights into the functions of Trx1 that are independent from its immediate function as a protein reductase.
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Affiliation(s)
- Tong Liu
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Changgong Wu
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Mohit Raja Jain
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Narayani Nagarajan
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Lin Yan
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Huacheng Dai
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Chuanlong Cui
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Ahmet Baykal
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Stacey Pan
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Tetsuro Ago
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Junichi Sadoshima
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States.
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Wezner-Ptasinska M, Otlewski J. Selection of specific interactors from phage display library based on sea lamprey variable lymphocyte receptor sequences. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1833-1841. [PMID: 26391289 DOI: 10.1016/j.bbapap.2015.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/06/2015] [Accepted: 09/17/2015] [Indexed: 12/31/2022]
Abstract
Variable lymphocyte receptors (VLRs) are non-immunoglobulin components of adaptive immunity in jawless vertebrates. These proteins composed of leucine-rich repeat modules offer some advantages over antibodies in target binding and therefore are attractive candidates for biotechnological applications. In this paper we report the design and characterization of a phage display library based on a previously proposed dVLR scaffold containing six LRR modules [Wezner-Ptasinska et al., 2011]. Our library was designed based on a consensus approach in which the randomization scheme reflects the frequencies of amino acids naturally occurring in respective positions responsible for antigen recognition. We demonstrate general applicability of the scaffold by selecting dVLRs specific for lysozyme and S100A7 protein with KD values in the micromolar range. The dVLR library could be used as a convenient alternative to antibodies for effective isolation of high affinity binders.
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Affiliation(s)
- Magdalena Wezner-Ptasinska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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Xie J, Bai X, Lavoie M, Lu H, Fan X, Pan X, Fu Z, Qian H. Analysis of the Proteome of the Marine Diatom Phaeodactylum tricornutum Exposed to Aluminum Providing Insights into Aluminum Toxicity Mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11182-11190. [PMID: 26308585 DOI: 10.1021/acs.est.5b03272] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Trace aluminum (Al) concentrations can be toxic to marine phytoplankton, the basis of the marine food web, but the fundamental Al toxicity and detoxification mechanisms at the molecular levels are poorly understood. Using an array of proteomic, transcriptomic, and biochemical techniques, we describe in detail the cellular response of the model marine diatom Phaeodactylum tricornutum to a short-term sublethal Al stress (4 h of exposure to 200 μM total initial Al). A total of 2204 proteins were identified and quantified by isobaric tags for relative and absolute quantification (iTRAQ) in response to the Al stress. Among them, 87 and 78 proteins performing various cell functions were up- and down-regulated after Al treatment, respectively. We found that photosynthesis was a key Al toxicity target. The Al-induced decrease in electron transport rates in thylakoid membranes lead to an increase in reactive oxygen species (ROS) production, which cause increased lipid peroxidation. Several ROS-detoxifying proteins were induced to help decrease Al-induced oxidative stress. In parallel, glycolysis and pentose phosphate pathway were up-regulated in order to produce cell energy (NADPH, ATP) and carbon skeleton for cell growth, partially circumventing the Al-induced toxicity effects on photosynthesis. These cellular responses to Al stress were coordinated by the activation of various signal transduction pathways. The identification of Al-responsive proteins in the model marine phytoplankton P. tricornutum provides new insights on Al stress responses as well as a good start for further exploring Al detoxification mechanisms.
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Affiliation(s)
- Jun Xie
- College of Biological and Environmental Engineering, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
| | - Xiaocui Bai
- Department of Food Science and Technology, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
| | - Michel Lavoie
- Quebec-Ocean and Takuvik Joint International Research Unit, Université Laval , Québec City, Québec G1V 0A6 Canada
| | - Haiping Lu
- College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. of China
| | - Xiaoji Fan
- College of Biological and Environmental Engineering, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese Academy of Sciences , Urumqi, Xinjiang 830011, P. R. of China
| | - Zhengwei Fu
- College of Biological and Environmental Engineering, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
| | - Haifeng Qian
- College of Biological and Environmental Engineering, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
- Department of Food Science and Technology, Zhejiang University of Technology , Hangzhou, Zhejiang 310032, P. R. of China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese Academy of Sciences , Urumqi, Xinjiang 830011, P. R. of China
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Latosinska A, Vougas K, Makridakis M, Klein J, Mullen W, Abbas M, Stravodimos K, Katafigiotis I, Merseburger AS, Zoidakis J, Mischak H, Vlahou A, Jankowski V. Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PLoS One 2015; 10:e0137048. [PMID: 26331617 PMCID: PMC4557910 DOI: 10.1371/journal.pone.0137048] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 08/12/2015] [Indexed: 11/18/2022] Open
Abstract
High resolution proteomics approaches have been successfully utilized for the comprehensive characterization of the cell proteome. However, in the case of quantitative proteomics an open question still remains, which quantification strategy is best suited for identification of biologically relevant changes, especially in clinical specimens. In this study, a thorough comparison of a label-free approach (intensity-based) and 8-plex iTRAQ was conducted as applied to the analysis of tumor tissue samples from non-muscle invasive and muscle-invasive bladder cancer. For the latter, two acquisition strategies were tested including analysis of unfractionated and fractioned iTRAQ-labeled peptides. To reduce variability, aliquots of the same protein extract were used as starting material, whereas to obtain representative results per method further sample processing and MS analysis were conducted according to routinely applied protocols. Considering only multiple-peptide identifications, LC-MS/MS analysis resulted in the identification of 910, 1092 and 332 proteins by label-free, fractionated and unfractionated iTRAQ, respectively. The label-free strategy provided higher protein sequence coverage compared to both iTRAQ experiments. Even though pre-fraction of the iTRAQ labeled peptides allowed for a higher number of identifications, this was not accompanied by a respective increase in the number of differentially expressed changes detected. Validity of the proteomics output related to protein identification and differential expression was determined by comparison to existing data in the field (Protein Atlas and published data on the disease). All methods predicted changes which to a large extent agreed with published data, with label-free providing a higher number of significant changes than iTRAQ. Conclusively, both label-free and iTRAQ (when combined to peptide fractionation) provide high proteome coverage and apparently valid predictions in terms of differential expression, nevertheless label-free provides higher sequence coverage and ultimately detects a higher number of differentially expressed proteins. The risk for receiving false associations still exists, particularly when analyzing highly heterogeneous biological samples, raising the need for the analysis of higher sample numbers and/or application of adjustment for multiple testing.
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Affiliation(s)
- Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Vougas
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Mahmoud Abbas
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Ioannis Katafigiotis
- Department of Urology, Medical School of Athens, Laikon Hospital, Athens, Greece
| | | | - Jerome Zoidakis
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vera Jankowski
- RWTH-Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
- * E-mail:
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