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Ahmadpour S, Habibi MA, Ghazi FS, Molazadeh M, Pashaie MR, Mohammadpour Y. The effects of tumor-derived supernatants (TDS) on cancer cell progression: A review and update on carcinogenesis and immunotherapy. Cancer Treat Res Commun 2024; 40:100823. [PMID: 38875884 DOI: 10.1016/j.ctarc.2024.100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/16/2024]
Abstract
Tumors can produce bioactive substances called tumor-derived supernatants (TDS) that modify the immune response in the host body. This can result in immunosuppressive effects that promote the growth and spread of cancer. During tumorigenesis, the exudation of these substances can disrupt the function of immune sentinels in the host and reinforce the support for cancer cell growth. Tumor cells produce cytokines, growth factors, and proteins, which contribute to the progression of the tumor and the formation of premetastatic niches. By understanding how cancer cells influence the host immune system through the secretion of these factors, we can gain new insights into cancer diagnosis and therapy.
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Affiliation(s)
- Sajjad Ahmadpour
- Patient Safety Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Mohammad Amin Habibi
- Department of Neurosurgery, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mikaeil Molazadeh
- Department of Medical Physics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Pashaie
- Patient Safety Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran; Department of Internal Medicine, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Yousef Mohammadpour
- Department of Medical Education, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
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2
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Keshavarz A, Salehi A, Khosravi S, Shariati Y, Nasrabadi N, Kahrizi MS, Maghsoodi S, Mardi A, Azizi R, Jamali S, Fotovat F. Recent findings on chimeric antigen receptor (CAR)-engineered immune cell therapy in solid tumors and hematological malignancies. Stem Cell Res Ther 2022; 13:482. [PMID: 36153626 PMCID: PMC9509604 DOI: 10.1186/s13287-022-03163-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/12/2022] [Indexed: 11/10/2022] Open
Abstract
Advancements in adoptive cell therapy over the last four decades have revealed various new therapeutic strategies, such as chimeric antigen receptors (CARs), which are dedicated immune cells that are engineered and administered to eliminate cancer cells. In this context, CAR T-cells have shown significant promise in the treatment of hematological malignancies. However, many obstacles limit the efficacy of CAR T-cell therapy in both solid tumors and hematological malignancies. Consequently, CAR-NK and CAR-M cell therapies have recently emerged as novel therapeutic options for addressing the challenges associated with CAR T-cell therapies. Currently, many CAR immune cell trials are underway in various human malignancies around the world to improve antitumor activity and reduce the toxicity of CAR immune cell therapy. This review will describe the comprehensive literature of recent findings on CAR immune cell therapy in a wide range of human malignancies, as well as the challenges that have emerged in recent years.
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Affiliation(s)
- Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Salehi
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Islamic Azad University,, Isfahan (Khorasgan) Branch, Isfahan, Iran
| | - Setareh Khosravi
- Department of Orthodontics, School of Dentistry, Alborz University of Medical Sciences, Karaj, Iran
| | - Yasaman Shariati
- Department of General Surgery, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Navid Nasrabadi
- Department of Endodontics, School of Dentistry, Birjand University of Medical Sciences, Birjand, Iran
| | | | - Sairan Maghsoodi
- Department of Paramedical, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Amirhossein Mardi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ramyar Azizi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samira Jamali
- Department of Endodontics, College of Stomatology, Stomatological Hospital, Xi’an Jiaotong University, Shaanxi, People’s Republic of China
| | - Farnoush Fotovat
- Department of Prosthodontics, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
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3
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CSNK2 in cancer: pathophysiology and translational applications. Br J Cancer 2022; 126:994-1003. [PMID: 34773100 PMCID: PMC8980014 DOI: 10.1038/s41416-021-01616-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Protein kinase CSNK2 (CK2) is a pleiotropic serine/threonine kinase frequently dysregulated in solid and hematologic malignancies. To consolidate a wide range of biological and clinically oriented data from this unique kinase in cancer, this systematic review summarises existing knowledge from in vitro, in vivo and pre-clinical studies on CSNK2 across 24 different human cancer types. CSNK2 mRNA transcripts, protein levels and activity were found to be routinely upregulated in cancer, and commonly identified phosphotargets included AKT, STAT3, RELA, PTEN and TP53. Phenotypically, it frequently influenced evasion of apoptosis, enhancement of proliferation, cell invasion/metastasis and cell cycle control. Clinically, it held prognostic significance across 14 different cancers, and its inhibition in xenograft experiments resulted in a positive treatment response in 12. In conjunction with commentary on preliminary studies of CSNK2 inhibitors in humans, this review harmonises an extensive body of CSNK2 data in cancer and reinforces its emergence as an attractive target for cancer therapy. Continuing to investigate CSNK2 will be crucial to advancing our understanding of CSNK2 biology, and offers the promise of important new discoveries scientifically and clinically.
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4
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Interaction between TMEFF1 and AHNAK proteins in ovarian cancer cells: Implications for clinical prognosis. Int Immunopharmacol 2022; 107:108726. [PMID: 35338959 DOI: 10.1016/j.intimp.2022.108726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022]
Abstract
TMEFF1 is a newly discovered protein involved in the physiological functions of the central nervous system, embryonic development, and other biological processes. Our previous study revealed that TMEFF1 acts as a tumor-promoting gene in ovarian cancer. AHNAK, as a giant scaffolding protein, plays a role in the formation of the blood-brain barrier, cell architecture and the regulation of cardiac calcium channels. However, its role in ovarian cancer remains poorly researched. In this study, we detected the expression of AHNAK and TMEFF1 in 148 different ovarian cancer tissues, determined their relationship with pathological parameters and prognosis, clarified the interaction between the two proteins, and explored the related cancer-promoting mechanisms through immunohistochemistry, immunoprecipitation, immunofluorescence double staining, western blotting, and bioinformatics. The high expression of ANHAK and TMEFF1 in ovarian cancer indicated a higher degree of tumor malignancy and a worse prognosis. Furthermore, the expression of TMEFF1 and AHNAK was significantly positively correlated. The results also showed that AHNAK and TMEFF1 co-localized and interacted with each other in ovarian cancer tissues and cells. And knockdown of AHNAK promoted proliferation, migration and invasion of ovarian cancer cells in vitro. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that AHNAK and related genes were enriched during mitosis regulation, cytoskeleton formation, gene epigenetics, etc., whereas TMEFF1 and related genes are enriched during immune regulation and other processes. We also clarified the network of kinases, microRNA, and transcription factor targets, and the impact of genetic mutations on prognosis. Notably, AHNAK was regulated by the expression of TMEFF1 and can activate the MAPK pathways. Overall, high expression of AHNAK and TMEFF1 in ovarian cancer cells indicated a higher degree of tumor malignancy and a worse prognosis. Therefore, the interaction between AHNAK and TMEFF1 may become a potential anti-tumor target for ovarian cancer treatment.
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5
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Hanoudi SN, Talwar H, Draghici S, Samavati L. Autoantibodies against cytoskeletons and lysosomal trafficking discriminate sarcoidosis from healthy controls, tuberculosis and lung cancers. MOLECULAR BIOMEDICINE 2022; 3:3. [PMID: 35048206 PMCID: PMC8770712 DOI: 10.1186/s43556-021-00064-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Sarcoidosis is a systemic granulomatous disease of unknown etiology. Hypergammaglobulinemia and the presence of autoantibodies in sarcoidosis suggest active humoral immunity to unknown antigen(s). We developed a complex cDNA library derived from tissues of sarcoidosis patients. Using a high throughput method, we constructed a microarray platform from this cDNA library containing large numbers of sarcoidosis clones. After selective biopanning, 1070 sarcoidosis-specifc clones were arrayed and immunoscreend with 152 sera from patients with sarcoidosis and other pulmonary diseases. To identify the sarcoidosis classifiers two statistical approaches were conducted: First, we identified significant biomarkers between sarcoidosis and healthy controls, and second identified markers comparing sarcoidosis to all other groups. At the threshold of an False Discovery Rate (FDR) < 0.01, we identified 14 clones in the first approach and 12 clones in the second approach discriminating sarcoidosis from other groups. We used the classifiers to build a naïve Bayes model on the training-set and validated it on an independent test-set. The first approach yielded an AUC of 0.947 using 14 significant clones with a sensitivity of 0.93 and specificity of 0.88, whereas the AUC of the second option was 0.92 with a sensitivity of 0.96 and specificity of 0.83. These results suggest robust classifier performance. Furthermore, we characterized the informative phage clones by sequencing and homology searches. Large numbers of classifier-clones were peptides involved in cellular trafficking and cytoskeletons. These results show that sarcoidosis is associated with a specific pattern of immunoreactivity that can discriminate it from other diseases.
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Affiliation(s)
| | - Harvinder Talwar
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine, 3990 John R, 3 Hudson, Detroit, MI 48201 USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI 48202 USA
| | - Lobelia Samavati
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine, 3990 John R, 3 Hudson, Detroit, MI 48201 USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI 48201 USA
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Roney MSI, Lanagan C, Sheng YH, Lawler K, Schmidt C, Nguyen NT, Begun J, Kijanka GS. IgM and IgA augmented autoantibody signatures improve early-stage detection of colorectal cancer prior to nodal and distant spread. Clin Transl Immunology 2021; 10:e1330. [PMID: 34603722 PMCID: PMC8473921 DOI: 10.1002/cti2.1330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/05/2023] Open
Abstract
Objectives Tumor‐associated autoantibodies (AAbs) in individuals with cancer can precede clinical diagnosis by several months to years. The objective of this study was to determine whether the primary immune response in form of IgM and gut mucosa‐associated IgA can aid IgG AAbs in the detection of early‐stage colorectal cancer (CRC). Methods We developed a novel protein array comprising 492 antigens seropositive in CRC. The array was used to profile IgG, IgM and IgA antibody signatures in 99 CRC patients and 99 sex‐ and age‐matched non‐cancer controls. A receiver operating curve (ROC), Kaplan–Meier survival analysis and univariate and multivariate Cox regression analyses were conducted. Results We identified a panel of 16 multi‐isotype AAbs with a cumulative sensitivity of 91% and specificity of 74% (AUC 0.90, 95% CI: 0.850–0.940) across all CRC stages. IgM and IgG isotypes were conversely associated with disease stage with IgM contributing significantly to improved stage I and II sensitivity of 96% at 78% specificity (AUC 0.928, 95% CI: 0.884–0.973). A single identified IgA AAb reached an overall sensitivity of 5% at 99% specificity (AUC 0.520, 95% CI: 0.440–0.601) balanced across all CRC stages. Kaplan–Meier analysis revealed that se33‐1 (ZNF638) IgG AAbs were associated with reduced 5‐year overall survival (log‐rank test, P = 0.012), whereas cumulative IgM isotype signatures were associated with improved 5‐year overall survival (log‐rank test, P = 0.024). Conclusion IgM AAbs are associated with early‐stage colorectal cancer. Combining IgG, IgM and IgA AAbs is a novel strategy to improve early diagnosis of cancers.
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Affiliation(s)
- Md Saiful Islam Roney
- Immune Profiling and Cancer Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia
| | - Catharine Lanagan
- Immune Profiling and Cancer Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia
| | - Yong Hua Sheng
- Inflammatory Bowel Diseases Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia
| | - Karen Lawler
- Pathology Queensland Queensland Health Brisbane QLD Australia
| | - Christopher Schmidt
- Immune Profiling and Cancer Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre Griffith University Brisbane QLD Australia
| | - Jakob Begun
- Inflammatory Bowel Diseases Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia.,School of Clinical Medicine Faculty of Medicine The University of Queensland Brisbane QLD Australia
| | - Gregor Stefan Kijanka
- Immune Profiling and Cancer Group Faculty of Medicine Mater Research Institute - The University of Queensland Translational Research Institute Woolloongabba QLD Australia.,Queensland Micro- and Nanotechnology Centre Griffith University Brisbane QLD Australia
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7
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Protein kinase CK2: a potential therapeutic target for diverse human diseases. Signal Transduct Target Ther 2021; 6:183. [PMID: 33994545 PMCID: PMC8126563 DOI: 10.1038/s41392-021-00567-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
CK2 is a constitutively active Ser/Thr protein kinase, which phosphorylates hundreds of substrates, controls several signaling pathways, and is implicated in a plethora of human diseases. Its best documented role is in cancer, where it regulates practically all malignant hallmarks. Other well-known functions of CK2 are in human infections; in particular, several viruses exploit host cell CK2 for their life cycle. Very recently, also SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been found to enhance CK2 activity and to induce the phosphorylation of several CK2 substrates (either viral and host proteins). CK2 is also considered an emerging target for neurological diseases, inflammation and autoimmune disorders, diverse ophthalmic pathologies, diabetes, and obesity. In addition, CK2 activity has been associated with cardiovascular diseases, as cardiac ischemia-reperfusion injury, atherosclerosis, and cardiac hypertrophy. The hypothesis of considering CK2 inhibition for cystic fibrosis therapies has been also entertained for many years. Moreover, psychiatric disorders and syndromes due to CK2 mutations have been recently identified. On these bases, CK2 is emerging as an increasingly attractive target in various fields of human medicine, with the advantage that several very specific and effective inhibitors are already available. Here, we review the literature on CK2 implication in different human pathologies and evaluate its potential as a pharmacological target in the light of the most recent findings.
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8
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Wang J, Zhao Y, Tang LL. Estimating the AUC with a Graphical Lasso Method for High-dimensional Biomarkers with LOD. BIOSTATISTICS & EPIDEMIOLOGY 2021; 5:189-206. [PMID: 35415380 PMCID: PMC9000202 DOI: 10.1080/24709360.2021.1898731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/13/2020] [Indexed: 06/14/2023]
Abstract
This manuscript estimates the area under the receiver operating characteristic curve (AUC) of combined biomarkers in a high-dimensional setting. We propose a penalization approach to the inference of precision matrices in the presence of the limit of detection. A new version of expectation-maximization algorithm is then proposed for the penalized likelihood, with the use of numerical integration and the graphical lasso method. The estimated precision matrix is then applied to the inference of AUCs. The proposed method outperforms the existing methods in numerical studies. We apply the proposed method to a data set of brain tumor study. The results show a higher accuracy on the estimation of AUC compared with the existing methods.
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Affiliation(s)
- Jirui Wang
- Department of Statistics, George Mason University
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9
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Xing L, Tian S, Mi W, Zhang Y, Zhang Y, Zhang Y, Xu F, Zhang C, Lou G. PRSS1 Upregulation Predicts Platinum Resistance in Ovarian Cancer Patients. Front Cell Dev Biol 2021; 8:618341. [PMID: 33585454 PMCID: PMC7876278 DOI: 10.3389/fcell.2020.618341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer is the most frequent cause of death among gynecologic malignancies. A total of 80% of patients who have completed platinum-based chemotherapy suffer from relapse and develop resistance within 2 years. In the present study, we obtained patients' complete platinum (cisplatin and carboplatin) medication information from The Cancer Genome Atlas database and then divided them into two categories: resistance and sensitivity. Difference analysis was performed to screen differentially expressed genes (DEgenes) related to platinum response. Subsequently, we annotated DEgenes into the protein–protein interaction network as seed nodes and analyzed them by random walk. Finally, second-ranking protease serine 1 gene (PRSS1) was selected as a candidate gene for verification analysis. PRSS1's expression pattern was continuously studied in Oncomine and cBio Cancer Genomic Portal databases, revealing the key roles of PRSS1 in ovarian cancer formation. Hereafter, we conducted in-depth explorations on PRSS1's platinum response to ovarian cancer through tissue and cytological experiments. Quantitative real-time polymerase chain reaction and Western blot assay results indicated that PRSS1 expression levels in platinum-resistant samples (tissue/cell) were significantly higher than in samples sensitive to platinum. By cell transfection assay, we observed that knockdown of PRSS1 reduced the resistance of ovarian cancer cells to cisplatin. Meanwhile, overexpression of PRSS1 increased the resistance to cisplatin. In conclusion, we identified a novel risk gene PRSS1 related to ovarian cancer platinum response and confirmed its key roles using multiple levels of low-throughput experiments, revealing a new treatment strategy based on a novel target factor for overcoming cisplatin resistance in ovarian cancer.
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Affiliation(s)
- Linan Xing
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Songyu Tian
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wanqi Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongjian Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yunyan Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuxi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fengye Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
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10
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Montero-Calle A, Barderas R. Analysis of Protein-Protein Interactions by Protein Microarrays. Methods Mol Biol 2021; 2344:81-97. [PMID: 34115353 DOI: 10.1007/978-1-0716-1562-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The analysis of the proteome and the interactome would be useful for a better understanding of the pathophysiology of several disorders, allowing the identification of potential specific markers for early diagnosis and prognosis, as well as potential targets of intervention. Among different proteomic approaches, high-density protein microarrays have become an interesting tool for the screening of protein-protein interactions and the interactome definition of disease-associated dysregulated proteins. This information might contribute to the identification of altered signaling pathways and protein functions involved in the pathogenesis of a disease. Remarkably, protein microarrays have been already satisfactorily employed for the study of protein-protein interactions in cancer, allergy, or neurodegenerative diseases. Here, we describe the utilization of recombinant protein microarrays for the identification of protein-protein interactions to help in the definition of disease-specific dysregulated interactomes.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Madrid, Spain.
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11
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Solís-Fernández G, Montero-Calle A, Alonso-Navarro M, Fernandez-Torres MÁ, Lledó VE, Garranzo-Asensio M, Barderas R, Guzman-Aranguez A. Protein Microarrays for Ocular Diseases. Methods Mol Biol 2021; 2344:239-265. [PMID: 34115364 DOI: 10.1007/978-1-0716-1562-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The eye is a multifaceted organ organized in several compartments with particular properties that reflect their diverse functions. The prevalence of ocular diseases is increasing, mainly because of its relationship with aging and of generalized lifestyle changes. However, the pathogenic molecular mechanisms of many common eye pathologies remain poorly understood. Considering the unquestionable importance of proteins in cellular processes and disease progression, proteomic techniques, such as protein microarrays, represent a valuable approach to analyze pathophysiological protein changes in the ocular environment. This technology enables to perform multiplex high-throughput protein expression profiling with minimal sample volume requirements broadening our knowledge of ocular proteome network in eye diseases.In this review, we present a brief summary of the main types of protein microarrays (antibody microarrays, reverse-phase protein microarrays, and protein microarrays) and their application for protein change detection in chronic ocular diseases such as dry eye, age-related macular degeneration, diabetic retinopathy, and glaucoma. The validation of these specific protein changes in eye pathologies may lead to the identification of new biomarkers, depiction of ocular disease pathways, and assistance in the diagnosis, prognosis, and development of new therapeutic options for eye pathologies.
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Affiliation(s)
- Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Leuven, Belgium
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Miren Alonso-Navarro
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Ángel Fernandez-Torres
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Victoria Eugenia Lledó
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - María Garranzo-Asensio
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain.
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12
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Hurley LC, Levin NK, Chatterjee M, Coles J, Muszkat S, Howarth Z, Dyson G, Tainsky MA. Evaluation of paraneoplastic antigens reveals TRIM21 autoantibodies as biomarker for early detection of ovarian cancer in combination with autoantibodies to NY-ESO-1 and TP53. Cancer Biomark 2020; 27:407-421. [PMID: 32083570 DOI: 10.3233/cbm-190988] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND The majority of ovarian cancer cases are diagnosed at an advanced stage with poor prognosis. This study evaluates autoantibodies against tumor antigens to identify candidate biomarkers for early detection of ovarian cancer in women at increased risk. OBJECTIVE To assess the immunoreactivity of paraneoplastic antigens and tumor associated antigens with high-grade serous ovarian cancer (HGSOC) samples. METHODS Five paraneoplastic antigens along with three tumor-associated antigens were evaluated with HGSOC patient serum samples. Validation screening was performed with n= 164 serum samples consisting of: 50 late stage HGSOC, 14 early stage HGSOC, 50 benign ovarian cyst, and 50 healthy control samples on ELISA and western blot. The four markers TRIM21, NY-ESO-1, TP53, and PAX8 were evaluated on a second validation serum set, n= 150. RESULTS TRIM21 achieved the highest sensitivity in the first validation screening of 33% with 100% specificity. Combining TRIM21 with NY-ESO-1, TP53, and PAX8 provided 67% sensitivity with 94% specificity, and 56% sensitivity at 98% specificity. These four markers resulted in 46% sensitivity with 98% specificity in the second validation cohort; TRIM21 achieved the highest individual sensitivity of 36%. CONCLUSIONS Autoantibodies to TRIM21, NY-ESO-1, and TP53 may complement CA125 in screening of women at genetic risk for ovarian cancer.
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Affiliation(s)
- Laura C Hurley
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Nancy K Levin
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA.,Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, USA
| | - Madhumita Chatterjee
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA.,Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, USA
| | - Jasmine Coles
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Shlomo Muszkat
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Zachary Howarth
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Gregory Dyson
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA.,Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, USA
| | - Michael A Tainsky
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA.,Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA.,Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, USA
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13
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Rauf F, Anderson KS, LaBaer J. Autoantibodies in Early Detection of Breast Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:2475-2485. [PMID: 32994341 PMCID: PMC7710604 DOI: 10.1158/1055-9965.epi-20-0331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
In spite of the progress made in treatment and early diagnosis, breast cancer remains a major public health issue worldwide. Although modern image-based screening modalities have significantly improved early diagnosis, around 15% to 20% of breast cancers still go undetected. In underdeveloped countries, lack of resources and cost concerns prevent implementing mammography for routine screening. Noninvasive, low-cost, blood-based markers for early breast cancer diagnosis would be an invaluable alternative that would complement mammography screening. Tumor-specific autoantibodies are excellent biosensors that could be exploited to monitor disease-specific changes years before disease onset. Although clinically informative autoantibody markers for early breast cancer screening have yet to emerge, progress has been made in the development of tools to discover and validate promising autoantibody signatures. This review focuses on the current progress toward the development of autoantibody-based early screening markers for breast cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Femina Rauf
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Karen S Anderson
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Joshua LaBaer
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona.
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14
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Ning L, Wang L, Zhang H, Jiao X, Chen D. Eukaryotic translation initiation factor 5A in the pathogenesis of cancers. Oncol Lett 2020; 20:81. [PMID: 32863914 PMCID: PMC7436936 DOI: 10.3892/ol.2020.11942] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer is the leading cause of death worldwide. The absence of obvious symptoms and insufficiently sensitive biomarkers in early stages of carcinoma limits early diagnosis. Cancer therapy agents and targeted therapy have been used extensively against tissues or organs of specific cancers. However, the intrinsic and/or acquired resistance to the agents or targeted drugs as well as the serious toxic side effects of the drugs would limit their use. Therefore, identifying biomarkers involved in tumorigenesis and progression represents a challenge for cancer diagnosis and therapeutic strategy development. The eukaryotic translation factor 5A (eIF5A), originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. There are two eIF5A isoforms (eIF5A1 and eIF5A2). eIF5A2 protein consists of 153 residues, and shares 84% amino acid identity with eIF5A1. However, the biological functions of these two isoforms may be significantly different. Recently, it was demonstrated that eIF5Ais widely involved in the pathogenesis of a number of diseases, including cancers. In particular, eIF5A plays an important role in regulating tumor growth, invasion, metastasis and tumor microenvironment. It was also shown to serve as a potential biomarker and target for the diagnosis and treatment of cancers. The present review briefly discusses the latest findings of eIF5A in the pathogenesis of certain malignant cancers and evolving clinical applications.
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Affiliation(s)
- Liang Ning
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Lei Wang
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Honglai Zhang
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xuelong Jiao
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Dong Chen
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
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15
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Kheirkhah R, DeMarshall C, Sieber F, Oh E, Nagele RG. The origin and nature of the complex autoantibody profile in cerebrospinal fluid. Brain Behav Immun Health 2020; 2:100032. [PMID: 38377421 PMCID: PMC8474157 DOI: 10.1016/j.bbih.2019.100032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/04/2023] Open
Abstract
The present study demonstrates, using human protein microarrays and plasma and cerebrospinal fluid samples obtained pre-surgically and simultaneously from 46 hip fracture repair patients, that CSF exhibits an extraordinarily complex IgG autoantibody profile composed of thousands of autoantibodies. We show that the pattern of expression levels of individual autoantibodies in CSF closely mimics that in the blood, regardless of age, gender or the presence or absence of disease, indicative of a blood-based origin for CSF autoantibodies. In addition, using five longitudinal serum samples obtained from one healthy individual over a span of nine years, we found that blood autoantibody profiles are remarkably stable over a long period of time, and that autoantibody profiles in both blood and CSF show features that are common among different individuals as well as individual-specific. Lastly, we demonstrate that an elevated CSF/plasma autoantibody ratio is more common in elderly hip fracture repair patients that experienced post-operative delirium than in non-delirium subjects, thus highlighting the crucial role that blood-brain and/or blood-CSF barrier compromise may play in the development of post-operative delirium.
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Affiliation(s)
- Rahil Kheirkhah
- Graduate School of Biomedical Sciences (GSBS), Rowan University, Stratford, NJ, USA
| | - Cassandra DeMarshall
- Biomarker Discovery Center, New Jersey Institute for Successful Aging, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
- Department of Geriatrics and Gerontology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
| | - Frederick Sieber
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins Bayview Medical Center, Baltimore, MD, USA
| | - Esther Oh
- Department of Medicine, Psychiatry and Behavioral Sciences, Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert G Nagele
- Biomarker Discovery Center, New Jersey Institute for Successful Aging, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
- Department of Geriatrics and Gerontology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
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16
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Garranzo-Asensio M, Montero-Calle A, Solís-Fernández G, Barderas R, Guzman-Aranguez A. Protein Microarrays: Valuable Tools for Ocular Diseases Research. Curr Med Chem 2019; 27:4549-4566. [PMID: 31244416 DOI: 10.2174/0929867326666190627131300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/07/2019] [Accepted: 05/14/2019] [Indexed: 11/22/2022]
Abstract
The eye is a complex organ comprised of several compartments with exclusive and specialized properties that reflect their diverse functions. Although the prevalence of eye pathologies is increasing, mainly because of its correlation with aging and of generalized lifestyle changes, the pathogenic molecular mechanisms of many common ocular diseases remain poorly understood. Therefore, there is an unmet need to delve into the pathogenesis, diagnosis, and treatment of eye diseases to preserve ocular health and reduce the incidence of visual impairment or blindness. Proteomics analysis stands as a valuable tool for deciphering protein profiles related to specific ocular conditions. In turn, such profiles can lead to real breakthroughs in the fields of ocular science and ophthalmology. Among proteomics techniques, protein microarray technology stands out by providing expanded information using very small volumes of samples. In this review, we present a brief summary of the main types of protein microarrays and their application for the identification of protein changes in chronic ocular diseases such as dry eye, glaucoma, age-related macular degeneration, or diabetic retinopathy. The validation of these specific protein alterations could provide new biomarkers, disclose eye diseases pathways, and help in the diagnosis and development of novel therapies for eye pathologies.
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Affiliation(s)
- María Garranzo-Asensio
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
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17
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San Segundo-Acosta P, Montero-Calle A, Fuentes M, Rábano A, Villalba M, Barderas R. Identification of Alzheimer's Disease Autoantibodies and Their Target Biomarkers by Phage Microarrays. J Proteome Res 2019; 18:2940-2953. [PMID: 31136180 DOI: 10.1021/acs.jproteome.9b00258] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The characterization of the humoral response in Alzheimer's disease (AD) patients might aid in detecting the disease at early stages. We have combined phage display and protein microarrays to identify AD autoantibodies and their target biomarkers. After enrichment of the T7 phage display libraries from AD and healthy brain tissue mRNA in AD-specific phages, 1536 monoclonal phages were printed on microarrays to probe them with 8 AD and 8 healthy control sera. A total of 57 phages showed higher seroreactivity in AD. In total, 13 out of the 44 unique sequences displayed on the phages were selected for validation using 68 AD and 52 healthy control sera. Peptides from Anthrax toxin receptor 1, Nuclear protein 1, Glycogen phosphorylase, and Olfactory receptor 8J1 expressed in bacteria as HaloTag fusion proteins showed a statistically significant ability to discriminate between AD patients and controls. The identified panel of AD autoantibodies might provide new insights into the blood-based diagnosis of the disease.
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Affiliation(s)
- Pablo San Segundo-Acosta
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain.,Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
| | - Ana Montero-Calle
- Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
| | - Manuel Fuentes
- Proteomics Unit , Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL) , 37007 Salamanca , Spain.,Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400 , Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL) , 37007 Salamanca , Spain
| | - Alberto Rábano
- Alzheimer Disease Research Unit, CIEN Foundation , Queen Sofia Foundation Alzheimer Center , 28031 Madrid , Spain
| | - Mayte Villalba
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
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18
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Antony F, Deantonio C, Cotella D, Soluri MF, Tarasiuk O, Raspagliesi F, Adorni F, Piazza S, Ciani Y, Santoro C, Macor P, Mezzanzanica D, Sblattero D. High-throughput assessment of the antibody profile in ovarian cancer ascitic fluids. Oncoimmunology 2019; 8:e1614856. [PMID: 31428516 DOI: 10.1080/2162402x.2019.1614856] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of effective biomarkers for early diagnosis, prognosis, and response to treatments remains a challenge in ovarian cancer (OC) research. Here, we present an unbiased high-throughput approach to profile ascitic fluid autoantibodies in order to obtain a tumor-specific antigen signature in OC. We first reported the reactivity of immunoglobulins (Igs) purified from OC patient ascites towards two different OC cell lines. Using a discovery set of Igs, we selected tumor-specific antigens from a phage display cDNA library. After biopanning, 700 proteins were expressed as fusion protein and used in protein array to enable large-scale immunoscreening with independent sets of cancer and noncancerous control. Finally, the selected antigens were validated by ELISA. The initial screening identified eight antigenic clones: CREB3, MRPL46, EXOSC10, BCOR, HMGN2, HIP1R, OLFM4, and KIAA1755. These antigens were all validated by ELISA in a study involving ascitic Igs from 153 patients (69 with OC, 34 with other cancers and 50 without cancer), with CREB3 showing the highest sensitivity (86.95%) and specificity (98%). Notably, we were able to identify an association between the tumor-associated (TA) antibody response and the response to a first-line tumor treatment (platinum-based chemotherapy). A stronger association was found by combining three antigens (BCOR, CREB3, and MRLP46) as a single antibody signature. Measurement of an ascitic fluid antibody response to multiple TA antigens may aid in the identification of new prognostic signatures in OC patients and shift attention to new potentially relevant targets.
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Affiliation(s)
- Frank Antony
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Cecilia Deantonio
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Diego Cotella
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Maria Felicia Soluri
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Olga Tarasiuk
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | | | - Fulvio Adorni
- Epidemiology Unit, Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Silvano Piazza
- Bioinformatics and Functional Genomics Unit, Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Area Science Park Trieste, Italy
| | - Yari Ciani
- Bioinformatics and Functional Genomics Unit, Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Area Science Park Trieste, Italy
| | - Claudio Santoro
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Paolo Macor
- Department of Life Science, University of Trieste, Trieste, Italy
| | - Delia Mezzanzanica
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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19
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Huang L, Li J. Weighted volume under the three-way receiver operating characteristic surface. Stat Methods Med Res 2018; 28:3627-3648. [PMID: 30453845 DOI: 10.1177/0962280218812211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
It is often necessary to differentiate subjects from multiple categories using medical tests. We may then adopt statistical measures to characterize the performance of these tests. The three-way ROC analysis has been proposed to evaluate the diagnostic accuracy of medical tests with three categories, reflecting the correct classification probabilities across all possible decision thresholds. The geometry of the ROC surface is carefully studied, leading to numerical summary measures such as the volume under the surface. This paper generalizes the global volume under the surface of three-way ROC analysis to the weighted volume under the surface (WVUS) by introducing a weight function emphasizing particular regions of correct classification probabilities. This generalization practically allows researchers to calculate the diagnostic accuracy for a medical or clinical biomarker while satisfactorily high probabilities of correct classification for one or two classes are conditionally ensured. We provide the asymptotic properties of the proposed nonparametric and parametric estimators of WVUS, which could easily lend support to statistical inferences. Some simulations have been conducted to assess the proposed estimators and also to demonstrate the necessity of WVUS. A real data analysis about liver cancer illustrates our methodology.
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Affiliation(s)
- Lei Huang
- Southwest Jiaotong University, School of Mathematics, Department of Statistics, Chengdu, China
| | - Jialiang Li
- Duke University NUS Graduate Medical School, Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore
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20
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Baldin AV, Grishina AN, Korolev DO, Kuznetsova EB, Golovastova MO, Kalpinskiy AS, Alekseev BY, Kaprin AD, Zinchenko DV, Savvateeva LV, Varshavsky VA, Zernii EY, Vinarov AZ, Bazhin AV, Philippov PP, Zamyatnin AA. Autoantibody against arrestin-1 as a potential biomarker of renal cell carcinoma. Biochimie 2018; 157:26-37. [PMID: 30389514 DOI: 10.1016/j.biochi.2018.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/25/2018] [Indexed: 12/28/2022]
Abstract
Renal cell carcinoma (RCC) is the second-most common uronephrological cancer. In the absence of specific symptoms, early diagnosis of RCC is challenging. Monitoring of the aberrant expression of tumour-associated antigens (TAAs) and related autoantibody response is considered as a novel approach of RCC diagnostics. The aim of this study was to examine the aberrant expression of arrestin-1 in renal tumours, to investigate the possible epigenetic mechanism underlying arrestin-1 expression, and to assess the frequency of anti-arrestin-1 autoantibody response. Immunohistochemistry was used to assess the presence of arrestin-1 in primary tumours and metastases of 39 patients with RCC and renal oncocytoma. Bisulfite sequencing was employed to analyse the methylation status of the promoter of the SAG gene encoding arrestin-1. Western blot analysis was performed to detect autoantibodies against arrestin-1 in serum samples of 36 RCC and oncocytoma patients. Arrestin-1 was found to be expressed in RCC (58.7% of cases) and renal oncocytoma (90% of cases) cells, while being absent in healthy kidney. The expression of arrestin-1 in RCC metastases was more prominent than in primary tumours. Hypomethylation of the SAG gene promoter is unlikely to be the mechanism for the aberrant expression of arrestin-1. Autoantibodies against arrestin-1 were detected in sera of 75% of RCC patients. Taken together, our findings suggest employment of autoantibody against arrestin-1 as biomarker of RCC.
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Affiliation(s)
- Alexey V Baldin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alena N Grishina
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Dmitry O Korolev
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Research Centre for Medical Genetics, 115522, Moscow, Russia.
| | - Marina O Golovastova
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexey S Kalpinskiy
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Boris Y Alekseev
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Andrey D Kaprin
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia.
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Vladimir A Varshavsky
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Evgeni Yu Zernii
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - Andrey Z Vinarov
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alexandr V Bazhin
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pavel P Philippov
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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21
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Hussain S, Saxena S, Shrivastava S, Arora R, Singh RJ, Jena SC, Kumar N, Sharma AK, Sahoo M, Tiwari AK, Mishra BP, Singh RK. Multiplexed Autoantibody Signature for Serological Detection of Canine Mammary Tumours. Sci Rep 2018; 8:15785. [PMID: 30361548 PMCID: PMC6202347 DOI: 10.1038/s41598-018-34097-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
Spontaneously occurring canine mammary tumours (CMTs) are the most common neoplasms of female unspayed dogs and are of potential importance as models for human breast cancer as well. Mortality rates are thrice higher in dogs as compared to humans with breast cancer, which can partly be attributed to lack of diagnostic techniques for their early detection. Human breast cancer studies reveal role of autoantibodies in early cancer diagnosis and also the usefulness of autoantibody panels in increasing the sensitivity, as well as, specificity of diagnostic assays. Therefore, in this study, we took advantage of high-throughput Luminex technique for developing a multiplex assay to detect autoantibody signatures against 5 canine mammary tumour-associated autoantigens (TAAs). These TAAs were expressed separately as fusion proteins with halo tag at the N-terminus, which allows easy and specific covalent coupling with magnetic microspheres. The multiplex assay, comprising a panel of candidate autoantigens (TPI, PGAM1, MNSOD, CMYC & MUC1) was used for screening circulating autoantibodies in 125 dog sera samples, including 75 mammary tumour sera and 50 healthy dog sera. The area under curve (AUC) of the combined panel of biomarkers is 0.931 (p < 0.0001), which validates the discriminative potential of the panel in differentiating tumour patients from healthy controls. The assay could be conducted in 3hrs using only 1ul of serum sample and could detect clinical cases of canine mammary tumour with sensitivity and specificity of 78.6% and 90%, respectively. In this study, we report for the first time a multiplexed assay for detection of autoantibodies in canine tumours, utilizing luminex technology and halo-tag coupling strategy. Further to the best of our knowledge, autoantibodies to CMYC and MUC1 have been reported for the first time in canines in this study.
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Affiliation(s)
- Shahid Hussain
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Sonal Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India.
| | - Sameer Shrivastava
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India.
| | - Richa Arora
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Rajkumar James Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Subas Chandra Jena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Naveen Kumar
- Division of Veterinary Surgery, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Anil Kumar Sharma
- Division of Veterinary Pathology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Monalisa Sahoo
- Division of Veterinary Pathology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Ashok Kumar Tiwari
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University] Izatnagar, Bareilly, UP, India.
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22
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Chatterjee M, Hurley LC, Levin NK, Stack M, Tainsky MA. Utility of paraneoplastic antigens as biomarkers for surveillance and prediction of recurrence in ovarian cancer. Cancer Biomark 2018; 20:369-387. [PMID: 29125478 DOI: 10.3233/cbm-170652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Ovarian cancer is frequently diagnosed at an advanced stage and 70% of patients experience recurrence months to years from initial diagnosis. The expression of paraneoplastic antigens can result in the occurrence of onconeural autoantibodies in ovarian cancer that may be associated with neurological disorders that are clinically manifested in patients before diagnosis of ovarian cancer. These paraneoplastic antigens can serve as excellent biomarkers not only for early detection but also for monitoring ovarian cancer recurrence. OBJECTIVE To assess the immunoreactivity of our previous 3 biomarkers along with 3 paraneoplastic antigens, HARS, Ro52 and CDR2 for the evaluation of their sensitivity in predicting recurrence before the clinical relapse of the ovarian cancer. METHODS Western blot immunoassays were performed to assess the immunoreactivity of 6 antigens with 21 recurrent ovarian cancer patients. RESULTS The results indicated that antibodies to HARS, Ro52, CDR2 and 5H6 antigens predicted ovarian cancer recurrence 5.03 months before the clinical or symptomatic relapse in 21 ovarian cancer patients with a sensitivity of 90.5% when CA125 levels were below the standard cutoff (35 U/ml). CONCLUSION Our study suggests that appearance of onconeural antibodies prior to the rise in CA125 during post treatment surveillance can be a useful diagnostic to predict ovarian cancer recurrence.
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Affiliation(s)
- Madhumita Chatterjee
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Laura C Hurley
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Nancy K Levin
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Matthew Stack
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A Tainsky
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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23
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San Segundo-Acosta P, Garranzo-Asensio M, Oeo-Santos C, Montero-Calle A, Quiralte J, Cuesta-Herranz J, Villalba M, Barderas R. High-throughput screening of T7 phage display and protein microarrays as a methodological approach for the identification of IgE-reactive components. J Immunol Methods 2018; 456:44-53. [PMID: 29470975 DOI: 10.1016/j.jim.2018.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/10/2018] [Accepted: 02/16/2018] [Indexed: 01/02/2023]
Abstract
Olive pollen and yellow mustard seeds are major allergenic sources with high clinical relevance. To aid with the identification of IgE-reactive components, the development of sensitive methodological approaches is required. Here, we have combined T7 phage display and protein microarrays for the identification of allergenic peptides and mimotopes from olive pollen and mustard seeds. The identification of these allergenic sequences involved the construction and biopanning of T7 phage display libraries of mustard seeds and olive pollen using sera from allergic patients to both biological sources together with the construction of phage microarrays printed with 1536 monoclonal phages from the third/four rounds of biopanning. The screening of the phage microarrays with individual sera from allergic patients enabled the identification of 10 and 9 IgE-reactive unique amino acid sequences from olive pollen and mustard seeds, respectively. Five immunoreactive amino acid sequences displayed on phages were selected for their expression as His6-GST tag fusion proteins and validation. After immunological characterization, we assessed the IgE-reactivity of the constructs. Our results show that protein microarrays printed with T7 phages displaying peptides from allergenic sources might be used to identify allergenic components -peptides, proteins or mimotopes- through their screening with specific IgE antibodies from allergic patients.
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Affiliation(s)
- Pablo San Segundo-Acosta
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain
| | - María Garranzo-Asensio
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain
| | - Carmen Oeo-Santos
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain
| | - Ana Montero-Calle
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain
| | - Joaquín Quiralte
- Unidad de Alergia, Complejo Hospitalario de Jaén, 23007 Jaén, Spain
| | | | - Mayte Villalba
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Rodrigo Barderas
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, 28040 Madrid, Spain; UFIEC-ISCIII, 28220 Majadahonda (Madrid), Spain.
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24
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Talwar H, Hanoudi SN, Geamanu A, Kissner D, Draghici S, Samavati L. Detection of Cystic Fibrosis Serological Biomarkers Using a T7 Phage Display Library. Sci Rep 2017; 7:17745. [PMID: 29255267 PMCID: PMC5735098 DOI: 10.1038/s41598-017-18041-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/19/2017] [Indexed: 12/02/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder affecting the cystic fibrosis transmembrane conductance regulator (CFTR). CF is characterized by repeated lung infections leading to respiratory failure. Using a high-throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This library was biopanned to obtain 1070 potential antigens. A microarray platform was constructed and immunoscreened with sera from healthy (n = 49), lung cancer (LC) (n = 31) and CF (n = 31) subjects. We built 1,000 naïve Bayes models on the training sets. We selected the top 20 frequently significant clones ranked with student t-test discriminating CF antigens from healthy controls and LC at a False Discovery Rate (FDR) < 0.01. The performances of the models were validated on an independent validation set. The mean of the area under the receiver operating characteristic (ROC) curve for the classifiers was 0.973 with a sensitivity of 0.999 and specificity of 0.959. Finally, we identified CF specific clones that correlate highly with sweat chloride test, BMI, and FEV1% predicted values. For the first time, we show that CF specific serological biomarkers can be identified through immunocreenings of a T7 phage display library with high accuracy, which may have utility in development of molecular therapy.
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Affiliation(s)
- Harvinder Talwar
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Samer Najeeb Hanoudi
- Department of Computer Science, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA
| | - Andreea Geamanu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Dana Kissner
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA
| | - Lobelia Samavati
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA. .,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E, Canfield, Detroit, MI, 48201, USA.
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25
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Wilson AL, Moffitt LR, Duffield N, Rainczuk A, Jobling TW, Plebanski M, Stephens AN. Autoantibodies against HSF1 and CCDC155 as Biomarkers of Early-Stage, High-Grade Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev 2017; 27:183-192. [PMID: 29141850 DOI: 10.1158/1055-9965.epi-17-0752] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/23/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Tumor-directed circulating autoantibodies (AAb) are a well-established feature of many solid tumor types, and are often observed prior to clinical disease manifestation. As such, they may provide a good indicator of early disease development. We have conducted a pilot study to identify novel AAbs as markers of early-stage HGSOCs.Methods: A rare cohort of patients with early (FIGO stage Ia-c) HGSOCs for IgG, IgA, and IgM-mediated AAb reactivity using high-content protein arrays (containing 9,184 individual proteins). AAb reactivity against selected antigens was validated by ELISA in a second, independent cohort of individual patients.Results: A total of 184 antigens were differentially detected in early-stage HGSOC patients compared with all other patient groups assessed. Among the six most highly detected "early-stage" antigens, anti-IgA AAbs against HSF1 and anti-IgG AAbs CCDC155 (KASH5; nesprin 5) were significantly elevated in patients with early-stage malignancy. Receiver operating characteristic (ROC) analysis suggested that AAbs against HSF1 provided better detection of early-stage malignancy than CA125 alone. Combined measurement of anti-HSF1, anti-CCDC155, and CA125 also improved efficacy at higher sensitivity.Conclusions: The combined measurement of anti-HSF1, anti-CCDC155, and CA125 may be useful for early-stage HGSOC detection.Impact: This is the first study to specifically identify AAbs associated with early-stage HGSOC. The presence and high frequency of specific AAbs in early-stage cancer patients warrants a larger scale examination to define their value for early disease detection at primary diagnosis and/or recurrence. Cancer Epidemiol Biomarkers Prev; 27(2); 183-92. ©2017 AACR.
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Affiliation(s)
- Amy L Wilson
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Laura R Moffitt
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Nadine Duffield
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Adam Rainczuk
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Tom W Jobling
- Obstetrics and Gynaecology, Monash Medical Centre, Clayton, Victoria, Australia.,Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia
| | - Magdalena Plebanski
- Department of Immunology and Pathology, Monash University, Melbourne, Australia.,School of Health and Biomedical Sciences, RMIT, Bundoora, Victoria, Australia
| | - Andrew N Stephens
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia. .,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia.,Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia
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26
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Tainsky MA, Chatterjee M, Levin NK, Draghici S, Abrams J. Multianalyte Tests for the Early Detection of Cancer: Speedbumps and Barriers. Biomark Insights 2017. [DOI: 10.1177/117727190700200037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
It has become very clear that a single molecular event is inadequate to accurately predict the biology (or pathophysiology) of cancer. Furthermore, using any single molecular event as a biomarker for the early detection of malignancy may not comprehensively identify the majority of individuals with that disease. Therefore, the fact that technologies have arisen that can simultaneously detect several, possibly hundreds, of biomarkers has propelled the field towards the development of multianalyte-based in vitro diagnostic early detection tests for cancer using body fluids such as serum, plasma, sputum, saliva, or urine. These multianalyte tests may be based on the detection of serum autoantibodies to tumor antigens, the presence of cancer-related proteins in serum, or the presence of tumor-specific genomic changes that appear in plasma as free DNA. The implementation of non-invasive diagnostic approaches to detect early stage cancer may provide the physician with evidence of cancer, but the question arises as to how the information will affect the pathway of clinical intervention. The confirmation of a positive result from an in vitro diagnostic cancer test may involve relatively invasive procedures to establish a true cancer diagnosis. If in vitro diagnostic tests are proven to be both specific, i.e. rarely produce false positive results due to unrelated conditions, and sufficiently sensitive, i.e. rarely produce false negative results, then such screening tests offer the potential for early detection and personalized therapeutics using multiple disease-related targets with convenient and non-invasive means. Here we discuss the technical and regulatory barriers inherent in development of clinical multianalyte biomarker assays.
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Affiliation(s)
- Michael A. Tainsky
- Program in Molecular Biology and Genetics, Karmanos Cancer Institute/Wayne State University, 110 E. Warren, Detroit, MI 48201
| | - Madhumita Chatterjee
- Program in Molecular Biology and Genetics, Karmanos Cancer Institute/Wayne State University, 110 E. Warren, Detroit, MI 48201
| | - Nancy K. Levin
- Program in Molecular Biology and Genetics, Karmanos Cancer Institute/Wayne State University, 110 E. Warren, Detroit, MI 48201
| | - Sorin Draghici
- Program in Molecular Biology and Genetics, Karmanos Cancer Institute/Wayne State University, 110 E. Warren, Detroit, MI 48201
- Department of Computer Science, Wayne State University, 5143 Cass Ave, Room 408 State Hall, Detroit, MI 48202
| | - Judith Abrams
- Integrated Biostatistics Core, Barbara Ann Karmanos Cancer Institute and Wayne State University, 428 HWCRC, 4100 John R, Detroit, MI 48201
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Sánchez-Silva DM, Acosta-Mesa HG, Romo-González T. Semi-Automatic Analysis for Unidimensional Immunoblot Images to Discriminate Breast Cancer Cases Using Time Series Data Mining. INT J PATTERN RECOGN 2017. [DOI: 10.1142/s0218001418600042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Breast cancer (BC) is one of the leading causes of death in adult women worldwide and the best way to reduce mortality and improve prognosis is through early diagnosis. Thus, it is necessary to optimize diagnostic methods; one option could be the automatic detection of patterns in 1D-II. In that respect, through recent analysis of unidimensional Immunoblot Images (1D-II), it was possible to distinguish between women with and without breast disease using as a discrimination criterion the presence of autoantibodies (bands) in their blood. However, the analysis of 1D-II is a difficult task even for an expert, generating great subjectivity and complexity in the process of interpretation. In the present study, a semi-automatic methodology for the bands’ analysis contained in the 1D-II’s was implemented and evaluated, the bands were extracted using digital image processing techniques. This was possible through the recognition of banding patterns represented as time series to distinguish between three classes: women with breast cancer (BC), women with benign breast pathology (BBP) and women without breast pathology (H). The classification was performed using the machine learning algorithm k-nearest neighbors (KNN) with different parameters over the time series representation. The semi-automatic method here presented was able to reduce the time, complexity and subjectivity of the image analysis with the performance metrics compared, obtaining similar percentages for both representations. With the traditional analysis, binary representation [Accuracy 72.8%, Precision 73.42% for three classes (BC, BBP and H) and Accuracy 90.91% Accuracy 92.55% Sensitivity 93.57% and Specificity 92.99% for two classes (BC and H)], versus Time series representation [Accuracy 66.4%, Precision 67.07% for three classes (BC, BBP and H) and Accuracy 86.36% Accuracy 87.31% Sensitivity 95.86% and Specificity 85.56% for two classes (BC and H)].
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Affiliation(s)
- Diana M. Sánchez-Silva
- Centro de Investigación en Inteligencia Artificial, Universidad Veracruzana, Xalapa Veracruz, México
- Área de Biología y Salud Integral, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa Veracruz, México
| | - Héctor G. Acosta-Mesa
- Centro de Investigación en Inteligencia Artificial, Universidad Veracruzana, Xalapa Veracruz, México
| | - Tania Romo-González
- Área de Biología y Salud Integral, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa Veracruz, México
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Chatterjee M, Hurley LC, Tainsky MA. Paraneoplastic antigens as biomarkers for early diagnosis of ovarian cancer. Gynecol Oncol Rep 2017; 21:37-44. [PMID: 28653032 PMCID: PMC5476453 DOI: 10.1016/j.gore.2017.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/24/2022] Open
Abstract
Paraneoplastic syndromes are a group of rare disorders that can be triggered by an abnormal immune response to proteins from tumors of the lung, ovary, lymphatics, or breast. Paraneoplastic clinical syndromes affect < 1% of patients with cancer; however, the frequency of subclinical levels of paraneoplastic autoantibodies in asymptomatic patients with cancer is unknown. Numerous studies have reported that ovarian cancer patients show signs of paraneoplastic neurological syndromes (PNSs) before or after their cancers are diagnosed. PNSs arise from a tumor-elicited immune response against onconeural antigens that are shared by tissues of nervous system, muscle, and tumor cells. Studies on the serum IgGs obtained from ovarian cancer patients have indicated the presence of onconeural antibodies in the absence of any PNS symptoms. The occurrence of PNSs is low in ovarian cancer patients and it can be accompanied by onconeural antibodies. The diagnosis of PNSs is accompanied by a suspicion of a malignant tumor such that neurologists typically refer such patients for a tumor diagnostic workup. There will be tremendous utility if subclinical levels (without paraneoplastic neurological symptoms or myositis) of these autoantibodies to paraneoplastic antigens can be exploited to screen asymptomatic high-risk patients for ovarian cancer, and used as biomarkers in immunoassays for the early detection or recurrence of ovarian cancer. Ovarian cancer overall survival is likely to be improved with early detection. Therefore, a panel of onconeural antigens that can detect paraneoplastic autoantibodies in patient sera should provide diagnostic utility for an earlier therapeutic intervention. Here we review the usefulness of PNS and other paraneoplastic syndromes and their association with paraneoplastic antigens to exploit these autoantibody biomarkers to form diagnostic multi-analyte panels for early detection of ovarian cancer.
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Affiliation(s)
- Madhumita Chatterjee
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Laura C Hurley
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Michael A Tainsky
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, United States.,Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, United States.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, United States
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29
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Katchman BA, Chowell D, Wallstrom G, Vitonis AF, LaBaer J, Cramer DW, Anderson KS. Autoantibody biomarkers for the detection of serous ovarian cancer. Gynecol Oncol 2017; 146:129-136. [PMID: 28427776 DOI: 10.1016/j.ygyno.2017.04.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/24/2017] [Accepted: 04/07/2017] [Indexed: 12/30/2022]
Abstract
Objective The purpose of this study was to identify a panel of novel serum tumor antigen-associated autoantibody (TAAb) biomarkers for the diagnosis of high-grade serous ovarian cancer. METHODS To detect TAAb we probed high-density programmable protein microarrays (NAPPA) containing 10,247 antigens with sera from patients with serous ovarian cancer (n=30 cases/30 healthy controls) and measured bound IgG. We identified 735 promising tumor antigens and evaluated these with an independent set of serous ovarian cancer sera (n=30 cases/30 benign disease controls/30 healthy controls). Thirty-nine potential tumor autoantigens were identified and evaluated using an orthogonal programmable ELISA platform against a total of 153 sera samples (n=63 cases/30 benign disease controls/60 healthy controls). Sensitivities at 95% specificity were calculated and a classifier for the detection of high-grade serous ovarian cancer was constructed. RESULTS We identified 11-TAAbs (ICAM3, CTAG2, p53, STYXL1, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3) that distinguished high-grade serous ovarian cancer cases from healthy controls with a combined 45% sensitivity at 98% specificity. CONCLUSION These are potential circulating biomarkers for the detection of serous ovarian cancer, and warrant confirmation in larger clinical cohorts.
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Affiliation(s)
- Benjamin A Katchman
- Virginia G. Piper Center for Personal Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Diego Chowell
- Virginia G. Piper Center for Personal Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Garrick Wallstrom
- Virginia G. Piper Center for Personal Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Allison F Vitonis
- Department of Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personal Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Daniel W Cramer
- Department of Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Karen S Anderson
- Virginia G. Piper Center for Personal Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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30
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Xu X, Qiu J, Sun Y. The basics of CAR T design and challenges in immunotherapy of solid tumors - Ovarian cancer as a model. Hum Vaccin Immunother 2017; 13:1548-1555. [PMID: 28272967 DOI: 10.1080/21645515.2017.1291473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Chimeric antigen receptor T cells are T cells genetically engineered with CAR constructs which mainly contain scFV and TCR zeta chain. With promising development in blood cancers, CAR T trials are also applied in solid cancers. However, the treatment effect in solid cancers is lower than expected. This review summarizes difference of CAR T applications in solid and blood cancers. Future challenges of CAR T cell treatment in solid cancer are also discussed using ovarian cancer as an example.
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Affiliation(s)
- Xuequn Xu
- a Department of Obstetrics and Gynecology , Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University , Shanghai , China
| | - Jin Qiu
- a Department of Obstetrics and Gynecology , Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University , Shanghai , China
| | - Yi Sun
- a Department of Obstetrics and Gynecology , Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University , Shanghai , China
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31
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32
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Atak A, Mukherjee S, Jain R, Gupta S, Singh VA, Gahoi N, K P M, Srivastava S. Protein microarray applications: Autoantibody detection and posttranslational modification. Proteomics 2016; 16:2557-2569. [PMID: 27452627 DOI: 10.1002/pmic.201600104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/09/2016] [Accepted: 07/19/2016] [Indexed: 12/18/2022]
Abstract
The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.
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Affiliation(s)
- Apurva Atak
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shuvolina Mukherjee
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rekha Jain
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shabarni Gupta
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vedita Anand Singh
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Nikita Gahoi
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Manubhai K P
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Abstract
Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.
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34
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Abstract
Immune monitoring is critical in settings of infection, autoimmunity, and cancer, but our understanding of the diversity of the antibody immune repertoire has been limited to selected target antigens and epitopes. Development of new vaccines requires monitoring of B cell immunity and identification of candidate antigens. As vaccines become more complex, novel techniques are required for monitoring the diversity of the B cell immune response. Since antibodies recognize both linear and conformational protein and glycoprotein epitopes, recent advances in proteomic and glycomic technologies for rapid display of antigenic structures are leading to methods for proteome-wide immune monitoring. Here, we review different approaches for protein display for immune monitoring, and provide methods for in situ protein display for the rapid detection and validation of antibody repertoires.
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Affiliation(s)
- Radwa Ewaisha
- Center for Personalized Diagnostics, School of Life Sciences, The Biodesign Institute, Arizona State University, 876401, Tempe, AZ, 85287, USA
| | - Karen S Anderson
- Center for Personalized Diagnostics, School of Life Sciences, The Biodesign Institute, Arizona State University, 876401, Tempe, AZ, 85287, USA.
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35
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Nagatomo H, Kohri N, Akizawa H, Hoshino Y, Yamauchi N, Kono T, Takahashi M, Kawahara M. Requirement for nuclear autoantigenic sperm protein mRNA expression in bovine preimplantation development. Anim Sci J 2015; 87:457-61. [PMID: 26690724 DOI: 10.1111/asj.12538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/11/2015] [Accepted: 08/20/2015] [Indexed: 11/28/2022]
Abstract
Nuclear autoantigenic sperm protein (NASP) is associated with DNA replication, cell proliferation, and cell cycle progression through its specific binding to histones. The aim of this study was to examine the roles of NASP in bovine preimplantation embryonic development. Using NASP gene knockdown (KD), we confirmed the reduction of NASP messenger RNA (mRNA) expression during preimplantation development. NASP KD did not affect cleavage but significantly decreased development of embryos into the blastocyst stage. Furthermore, blastocyst hatching was significantly decreased in NASP KD embryos. Cell numbers in the inner cell mass of NASP KD blastocysts were also decreased compared to those of controls. These results suggest that NASP mRNA expression is required for preimplantation development into the blastocyst stage in cattle.
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Affiliation(s)
- Hiroaki Nagatomo
- Advanced Biotechnology Center, University of Yamanashi, Kofu, Japan
| | - Nanami Kohri
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroki Akizawa
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yumi Hoshino
- Laboratory of Animal Reproduction, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Nobuhiko Yamauchi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Tomohiro Kono
- Department of BioScience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masashi Takahashi
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Manabu Kawahara
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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36
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Futami J, Nonomura H, Kido M, Niidoi N, Fujieda N, Hosoi A, Fujita K, Mandai K, Atago Y, Kinoshita R, Honjo T, Matsushita H, Uenaka A, Nakayama E, Kakimi K. Sensitive Multiplexed Quantitative Analysis of Autoantibodies to Cancer Antigens with Chemically S-Cationized Full-Length and Water-Soluble Denatured Proteins. Bioconjug Chem 2015; 26:2076-84. [PMID: 26355635 DOI: 10.1021/acs.bioconjchem.5b00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Humoral immune responses against tumor-associated antigens (TAAs) or cancer/testis antigens (CTAs) aberrantly expressed in tumor cells are frequently observed in cancer patients. Recent clinical studies have elucidated that anticancer immune responses with increased levels of anti-TAA/CTA antibodies improve cancer survival rates. Thus, these antibody levels are promising biomarkers for diagnosing the efficiency of cancer immunotherapy. Full-length antigens are favored for detecting anti-TAA/CTA antibodies because candidate antigen proteins contain multiple epitopes throughout their structures. In this study, we developed a methodology to prepare purified water-soluble and full-length antigens by using cysteine sulfhydryl group cationization (S-cationization) chemistry. S-Cationized antigens can be prepared from bacterial inclusion bodies, and they exhibit improved protein solubility but preserved antigenicity. Anti-TAA/CTA antibodies detected in cancer patients appeared to recognize linear epitopes, as well as conformational epitopes, and because the frequency of cysteine side-residues on the epitope-paratope interface was low, any adverse effects of S-cationization were virtually negligible for antibody binding. Furthermore, S-cationized antigen-immobilized Luminex beads could be successfully used in highly sensitive quantitative-multiplexed assays. Indeed, patients with a more broadly induced serum anti-TAA/CTA antibody level showed improved progression-free survival after immunotherapy. The comprehensive anti-TAA/CTA assay system, which uses S-cationized full-length and water-soluble recombinant antigens, may be a useful diagnostic tool for assessing the efficiency of cancer immunotherapy.
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Affiliation(s)
- Junichiro Futami
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Hidenori Nonomura
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Momoko Kido
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Naomi Niidoi
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Nao Fujieda
- Medinet Co. Ltd. , Yokohama, Kanagawa 222-0033, Japan.,Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Akihiro Hosoi
- Medinet Co. Ltd. , Yokohama, Kanagawa 222-0033, Japan.,Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Kana Fujita
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Komako Mandai
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Yuki Atago
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Rie Kinoshita
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Tomoko Honjo
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Akiko Uenaka
- Faculty of Health and Welfare, Kawasaki University of Medical Welfare , Kurashiki, Okayama 701-0193, Japan
| | - Eiichi Nakayama
- Faculty of Health and Welfare, Kawasaki University of Medical Welfare , Kurashiki, Okayama 701-0193, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
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Development of a T7 Phage Display Library to Detect Sarcoidosis and Tuberculosis by a Panel of Novel Antigens. EBioMedicine 2015; 2:341-350. [PMID: 26086036 PMCID: PMC4465182 DOI: 10.1016/j.ebiom.2015.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sarcoidosis is a granulomatous inflammatory disease, diagnosed through tissue biopsy of involved organs in the absence of other causes such as tuberculosis (TB). No specific serologic test is available to diagnose and differentiate sarcoidosis from TB. Using a high throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This complex cDNA library was biopanned to obtain 1152 potential sarcoidosis antigens and a microarray was constructed to immunoscreen two different sets of sera from healthy controls and sarcoidosis. Meta-analysis identified 259 discriminating sarcoidosis antigens, and multivariate analysis identified 32 antigens with a sensitivity of 89% and a specificity of 83% to classify sarcoidosis from healthy controls. Additionally, interrogating the same microarray platform with sera from subjects with TB, we identified 50 clones that distinguish between TB, sarcoidosis and healthy controls. The top 10 sarcoidosis and TB specific clones were sequenced and homologies were searched in the public database revealing unique epitopes and mimotopes in each group. Here, we show for the first time that immunoscreenings of a library derived from sarcoidosis tissue differentiates between sarcoidosis and tuberculosis antigens. These novel biomarkers can improve diagnosis of sarcoidosis and TB, and may aid to develop or evaluate a TB vaccine. Immunity plays a major role in a vast array of human diseases. Sarcoidosis shares similarities with non-infectious and infectious granulomatous diseases, including tuberculosis. A highly sensitive and specific T7 phage library discriminates the immune signature between sarcoidosis patients and TB.
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Fang J, Wang H, Xi W, Cheng G, Wang S, Su S, Zhang S, Deng Y, Song Z, Xu A, Liu B, Cao J, Wang Z. Downregulation of tNASP inhibits proliferation through regulating cell cycle-related proteins and inactive ERK/MAPK signal pathway in renal cell carcinoma cells. Tumour Biol 2015; 36:5209-14. [PMID: 25669170 DOI: 10.1007/s13277-015-3177-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022] Open
Abstract
Nuclear auto-antigenic sperm protein (NASP), initially described as a highly auto-immunogenic testis and sperm-specific protein, is a histone chaperone that is proved to present in all dividing cells. NASP has two splice variants: testicular NASP (tNASP) and somatic form of NASP (sNASP). Only cancer, germ, transformed, and embryonic cells have a high level of expression of the tNASP. Up to now, little has been known about tNASP in renal cell carcinoma (RCC). In the present study, the molecular mechanism of tNASP in RCC was explored. The expression level of tNASP in 16 paired human RCC specimens was determined. Downregulation of tNASP by small interfering RNA (siRNA) was transfected in RCC cell lines. The effect of downregulation of tNASP by siRNA on cell colony formation and proliferation was examined by colony formation assay and CCK-8 assay, cell cycle was analyzed by flow cytometry, and the expression of cyclin D1 and P21 were detected by Western blotting. ERK/MAPK signaling was also analyzed. tNASP has a relative high expression level in human RCC tissues. Via upregulation of P21 and downregulation of cyclinD1, silence of tNASP can inhibit cell proliferation, which induces cell cycle arrest. Furthermore, ERK signaling pathway is confirmed to mediate the regulation of cell cycle-related proteins caused by silence of tNASP. Our research demonstrates that knockdown of tNASP effectively inhibits the proliferation and causes G1 phase arrest through ERK/MAPK signal pathway.
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Affiliation(s)
- Jianzheng Fang
- State Key Laboratory of Reproductive Medicine, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, China
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White NMA, Masui O, Desouza LV, Krakovska O, Metias S, Romaschin AD, Honey RJ, Stewart R, Pace K, Lee J, Jewett MA, Bjarnason GA, Siu KWM, Yousef GM. Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma. Oncotarget 2015; 5:506-18. [PMID: 24504108 PMCID: PMC3964225 DOI: 10.18632/oncotarget.1529] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
There are no serum biomarkers for the accurate diagnosis of clear cell renal cell carcinoma (ccRCC). Diagnosis and decision of nephrectomy rely on imaging which is not always accurate. Non-invasive diagnostic biomarkers are urgently required. In this study, we preformed quantitative proteomics analysis on a total of 199 patients including 30 matched pairs of normal kidney and ccRCC using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to identify differentially expressed proteins. We found 55 proteins significantly dysregulated in ccRCC compared to normal kidney tissue. 54 were previously reported to play a role in carcinogenesis, and 39 are secreted proteins. Dysregulation of alpha-enolase (ENO1), L-lactate dehydrogenase A chain (LDHA), heat shock protein beta-1 (HSPB1/Hsp27), and 10 kDa heat shock protein, mitochondrial (HSPE1) was confirmed in two independent sets of patients by western blot and immunohistochemistry. Pathway analysis, validated by PCR, showed glucose metabolism is altered in ccRCC compared to normal kidney tissue. In addition, we examined the utility of Hsp27 as biomarker in serum and urine. In ccRCC patients, Hsp27 was elevated in the urine and serum and high serum Hsp27 was associated with high grade (Grade 3-4) tumors. These data together identify potential diagnostic biomarkers for ccRCC and shed new light on the molecular mechanisms that are dysregulated and contribute to the pathogenesis of ccRCC. Hsp27 is a promising diagnostic marker for ccRCC although further large-scale studies are required. Also, molecular profiling may help pave the road to the discovery of new therapies.
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Affiliation(s)
- Nicole M A White
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and the Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
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Barderas R, Villar-Vázquez R, Casal JI. Colorectal Cancer Circulating Biomarkers. BIOMARKERS IN CANCER 2015. [DOI: 10.1007/978-94-007-7681-4_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Utility of Autoantibodies as Biomarkers for Diagnosis and Staging of Neurodegenerative Diseases. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 122:1-51. [DOI: 10.1016/bs.irn.2015.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Anderson KS, Cramer DW, Sibani S, Wallstrom G, Wong J, Park J, Qiu J, Vitonis A, LaBaer J. Autoantibody signature for the serologic detection of ovarian cancer. J Proteome Res 2014; 14:578-86. [PMID: 25365139 PMCID: PMC4334299 DOI: 10.1021/pr500908n] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sera from patients with ovarian cancer contain autoantibodies (AAb) to tumor-derived proteins that are potential biomarkers for early detection. To detect AAb, we probed high-density programmable protein microarrays (NAPPA) expressing 5177 candidate tumor antigens with sera from patients with serous ovarian cancer (n = 34 cases/30 controls) and measured bound IgG. Of these, 741 antigens were selected and probed with an independent set of ovarian cancer sera (n = 60 cases/60 controls). Twelve potential autoantigens were identified with sensitivities ranging from 13 to 22% at >93% specificity. These were retested using a Luminex bead array using 60 cases and 60 controls, with sensitivities ranging from 0 to 31.7% at 95% specificity. Three AAb (p53, PTPRA, and PTGFR) had area under the curve (AUC) levels >60% (p < 0.01), with the partial AUC (SPAUC) over 5 times greater than for a nondiscriminating test (p < 0.01). Using a panel of the top three AAb (p53, PTPRA, and PTGFR), if at least two AAb were positive, then the sensitivity was 23.3% at 98.3% specificity. AAb to at least one of these top three antigens were also detected in 7/20 sera (35%) of patients with low CA 125 levels and 0/15 controls. AAb to p53, PTPRA, and PTGFR are potential biomarkers for the early detection of ovarian cancer.
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Affiliation(s)
- Karen S Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287-6401, United States
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Minami S, Nagashio R, Ueda J, Matsumoto K, Goshima N, Hattori M, Hachimura K, Iwamura M, Sato Y. Detection of tumor-associated antigens in culture supernatants using autoantibodies in sera from patients with bladder cancer. Biomed Res 2014; 35:25-35. [PMID: 24573199 DOI: 10.2220/biomedres.35.25] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Secreted proteins play essential roles in the process of tumorigenesis, and the analysis of tumor-secreted proteins has been suggested as a promising strategy for identifying cancer biomarkers. In this study, we performed proteomic analysis to identify proteins secreted from bladder cancer cell lines that are recognized by autoantibodies in sera from patients with bladder cancer. In addition,autoantibodies against the identified proteins were validated using a dot-blot array with sera from patients with bladder cancer and normal controls. As the results, we detected twenty-five and thirty-two immunoreactive spots in sera from patients with high- and low-grade bladder cancer, respectively.In addition, validation analysis revealed that serum IgG levels of anti-calreticulin and matrix metalloproteinase-2 (MMP2) autoantibodies were significantly higher in bladder cancer patients than in normal controls (both P < 0.05). Furthermore, the serum IgG level of anti-MMP2 autoantibody was significantly higher in patients with high- compared to low-grade bladder cancer(P < 0.05). On multivariate analysis, the serum IgG level of anti-MMP2 autoantibody was an independent predictor of cancer-specific survival (P < 0.05). Based on these findings, serum IgG levels of anti-calreticulin and MMP2 autoantibodies may be novel biomarker candidates for bladder cancer and its clinical outcome.
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Affiliation(s)
- Sho Minami
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Kitasato1-15-1,Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
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Abstract
In addition to their historical role, autoantibodies appear promising as biomarkers to facilitate diagnosis, improve patient outcome and decrease mortality in cancer. Autoantibodies may also be useful in the identification of subjects at risk for cancer, that is, those bearing premalignant changes. Numerous studies have demonstrated that cancer serum contains a variety of autoantibodies that react with autologous cellular antigens, that is, tumor-associated antigens. Interestingly, some of these antigens are involved in signal transduction, cell cycle regulation, cell proliferation, and apoptosis. As such, identification of these molecules has additional importance for development of novel anticancer drugs and vaccines. This review focuses on the use of autoantibodies in breast cancer, a major public health problem. We also address the need for additional research to validate this approach in cancer diagnostics and therapeutics in general.
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von Boxberg Y, Soares S, Féréol S, Fodil R, Bartolami S, Taxi J, Tricaud N, Nothias F. Giant scaffolding protein AHNAK1 interacts with β-dystroglycan and controls motility and mechanical properties of Schwann cells. Glia 2014; 62:1392-406. [PMID: 24796807 DOI: 10.1002/glia.22685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 04/11/2014] [Accepted: 04/17/2014] [Indexed: 01/02/2023]
Abstract
The profound morphofunctional changes that Schwann cells (SCs) undergo during their migration and elongation on axons, as well as during axon sorting, ensheathment, and myelination, require their close interaction with the surrounding laminin-rich basal lamina. In contrast to myelinating central nervous system glia, SCs strongly and constitutively express the giant scaffolding protein AHNAK1, localized essentially underneath the outer, abaxonal plasma membrane. Using electron microscopy, we show here that in the sciatic nerve of ahnak1(-) (/) (-) mice the ultrastructure of myelinated, and unmyelinated (Remak) fibers is affected. The major SC laminin receptor β-dystroglycan co-immunoprecipitates with AHNAK1 shows reduced expression in ahnak1(-) (/) (-) SCs, and is no longer detectable in Cajal bands on myelinated fibers in ahnak1(-) (/) (-) sciatic nerve. Reduced migration velocity in a scratch wound assay of purified ahnak1(-) (/) (-) primary SCs cultured on a laminin substrate indicated a function of AHNAK1 in SC motility. This was corroborated by atomic force microscopy measurements, which revealed a greater mechanical rigidity of shaft and leading tip of ahnak1(-) (/) (-) SC processes. Internodal lengths of large fibers are decreased in ahnak1(-) (/) (-) sciatic nerve, and longitudinal extension of myelin segments is even more strongly reduced after acute knockdown of AHNAK1 in SCs of developing sciatic nerve. Together, our results suggest that by interfering in the cross-talk between the transmembrane form of the laminin receptor dystroglycan and F-actin, AHNAK1 influences the cytoskeleton organization of SCs, and thus plays a role in the regulation of their morphology and motility and lastly, the myelination process.
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Affiliation(s)
- Ysander von Boxberg
- Sorbonne Universités, UPMC CR18 (NPS), Paris, France; Neuroscience Paris Seine (NPS), CNRS UMR 8246, Paris, France; Neuroscience Paris Seine (NPS), INSERM U1130, Paris, France
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Blood autoantibodies against tumor-associated antigens as biomarkers in early detection of colorectal cancer. Cancer Lett 2014; 346:178-87. [DOI: 10.1016/j.canlet.2014.01.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/07/2014] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
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Kundeti V, Rajasekaran S, Dinh H. Border length minimization problem on a square array. J Comput Biol 2014; 21:446-55. [PMID: 24528000 DOI: 10.1089/cmb.2013.0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein/peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and high-throughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having low serum titers, and locate antibody signatures. Improving the yield of microarray fabrication involves solving a hard combinatorial optimization problem called the border length minimization problem (BLMP). An important question that remained open for the past 7 years is if the BLMP is tractable or not. We settle this open problem by proving that the BLMP is [Formula: see text]-hard. We also present a hierarchical refinement algorithm that can refine any heuristic solution for the BLMP and prove that the TSP+1-threading heuristic is an O(N)-approximation.
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Affiliation(s)
- Vamsi Kundeti
- Computer Science and Engineering Department, University of Connecticut , Storrs, CT
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Lin HS, Siddiq F, Talwar HS, Chen W, Voichita C, Draghici S, Jeyapalan G, Chatterjee M, Fribley A, Yoo GH, Sethi S, Kim H, Sukari A, Folbe AJ, Tainsky MA. Serum prognostic biomarkers in head and neck cancer patients. Laryngoscope 2014; 124:1819-26. [PMID: 24347532 DOI: 10.1002/lary.24567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVES/HYPOTHESIS A reliable estimate of survival is important as it may impact treatment choice. The objective of this study is to identify serum autoantibody biomarkers that can be used to improve prognostication for patients affected with head and neck squamous cell carcinoma (HNSCC). STUDY DESIGN Prospective cohort study. METHODS A panel of 130 serum biomarkers, previously selected for cancer detection using microarray-based serological profiling and specialized bioinformatics, were evaluated for their potential as prognostic biomarkers in a cohort of 119 HNSCC patients followed for up to 12.7 years. A biomarker was considered positive if its reactivity to the particular patient's serum was greater than one standard deviation above the mean reactivity to sera from the other 118 patients, using a leave-one-out cross-validation model. Survival curves were estimated according to the Kaplan-Meier method, and statistically significant differences in survival were examined using the log rank test. Independent prognostic biomarkers were identified following analysis using multivariate Cox proportional hazards models. RESULTS Poor overall survival was associated with African Americans (hazard ratio [HR] for death = 2.61; 95% confidence interval [CI]: 1.58-4.33; P = .000), advanced stage (HR = 2.79; 95% CI: 1.40-5.57; P = .004), and recurrent disease (HR = 6.66; 95% CI: 2.54-17.44; P = .000). On multivariable Cox analysis adjusted for covariates (race and stage), six of the 130 markers evaluated were found to be independent prognosticators of overall survival. CONCLUSIONS The results shown here are promising and demonstrate the potential use of serum biomarkers for prognostication in HNSCC patients. Further clinical trials to include larger samples of patients across multiple centers may be warranted.
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Affiliation(s)
- Ho-Sheng Lin
- Department of Surgery, John D. Dingell VA Medical Center, Detroit, Michigan, U.S.A; Department of Otolaryngology-Head and Neck Surgery, Barbara Ann Karmanos Cancer Institute/Wayne State University, Detroit, Michigan, U.S.A
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Ye B, Gagnon A, Mok SC. Recent technical strategies to identify diagnostic biomarkers for ovarian cancer. Expert Rev Proteomics 2014; 4:121-31. [PMID: 17288520 DOI: 10.1586/14789450.4.1.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ovarian cancer is the fifth leading cause of cancer deaths among North American women. Regrettably, there is currently no reliable circulating biomarker that can detect ovarian cancer in its early stages. The CA125 biomarker is very useful for treatment response monitoring, but its sensitivity is very low for early detection. Thus, there is an urgent need for the identification of new circulating biomarkers/panel of biomarkers that could be used to diagnose ovarian cancer before it becomes clinically detectable and advanced. Unfortunately, the strategies used in the past years to identify such biomarkers have not led to any outstanding candidate. This review summarizes the different approaches used in the last decade and suggests which strategies should be adopted in the near future in order to lead to the successful identification of new ovarian cancer diagnostic biomarkers.
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Affiliation(s)
- Bin Ye
- Harvard Medical School, Department of Obstetrics & Gynecology, Brigham & Women's Hospital, Dana-Farber Harvard Cancer Center, Boston, MA 02115, USA.
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Järås K, Anderson K. Autoantibodies in cancer: prognostic biomarkers and immune activation. Expert Rev Proteomics 2014; 8:577-89. [DOI: 10.1586/epr.11.48] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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